Autoimmune Disease and Gut Health: The Chicken or the Egg?

Adapted from episode 70 of The Perfect Stool podcast and edited for readability.

I’m going to start with some basics about autoimmune disease and then get into how it relates to gut health, because the two are all tied up together. 

For those who don’t know, autoimmune disease is where your immune system attacks your own body’s cells, tissues and organs. I personally have two autoimmune diseases, which you may have heard me talk about on other podcasts: Hashimoto’s thyroiditis and post-infectious IBS. The latter is when a protein called vinculin that’s involved with the migrating motor complex, attacks my small intestine, which creates stagnation in the small intestine and bacterial overgrowths. I did receive a third autoimmune diagnosis in 2013 of ITP or idiopathic thrombocytopenia, which is an autoimmune disease impacting your platelets. However, the doctor has subsequently told me he didn’t think I ever had it, as the diagnosis criteria have changed. And I was also diagnosed at one point with pernicious anemia, which is an autoimmune attack on the parietal cells lining the stomach, which leads to malabsorption of vitamin B12, but have since had negative antibodies there, so I don’t consider that a current diagnosis. 

If you think of individual autoimmune diseases like Hashimoto’s thyroiditis, lupus or rheumatoid arthritis, you may not think it’s all that common, but when you add up all the different autoimmune diseases, it comes to more than 50 million Americans impacted, which is a threefold increase in autoimmunity over the last 50 years. Interestingly 78% of those impacted by autoimmunity are women. 

Other than the ones I just mentioned, some of the other most common autoimmune diseases are Celiac disease, Grave’s disease, Type 1 Diabetes, vitiligo, scleroderma, psoriasis, inflammatory bowel disease, Addison’s disease and Sjögren’s. There are more than 100 autoimmune diseases that are either systemic or attack individual organs. 

Based on twin studies, about 25% of autoimmune disease can be attributed to genetic causes versus 75% environmental causes. In reality, it’s always a combination of genetic and environmental factors that lead to the manifestation of an autoimmune disease. Thanks to the work of Dr. Alessio Fassano, a world-renowned gastroenterologist and gluten intolerance expert who is chief of Pediatric Gastroenterology and Nutrition at MassGeneral Hospital for Children and Director of the Center for Celiac Research and Treatment, we know that there are three necessary precursors to autoimmunity:  a genetic predisposition, an exposure to a trigger such as trauma, stress, toxins, the use of certain medications or exposure to an antigen, and intestinal permeability or leaky gut.

Now before I delve deep into gut related infections and triggers, let me just mention the other autoimmune triggers. So in terms of antigens, which are toxins or other foreign substances that induce an immune response in the body, there are viruses like Epstein-Barr Virus, aka mononucleosis, including a reactivation of a prior infection, cytomegalovirus, mumps, rubella, Herpes simplex virus and Hepatitis C. Then toxins can come from your diet and the environment, including chemicals and heavy metals, which can provoke intestinal permeability and other gut health problems, which we discussed in my last podcast

In terms of medication-induced autoimmunity, one of the most common is drug-induced lupus, in which more than 90 medications from more than 10 drug classes have been implicated.  Don’t think this is just rare, unusual drugs.  There are case reports of drug-induced lupus from drugs as common as statins, antibiotics, PPIs and NSAIDs. And there are even reports of drugs used for other autoimmune diseases, called TNF blockers, that have induced lupus syndrome.

Other autoimmune diseases for which drugs have been implicated include RA, polymyositis, dermatomyositis, myasthenia gravis, pemphigus, pemphigoid, membranous glomerulonephritis, autoimmune hepatitis, autoimmune thyroiditis (Hashimoto’s), autoimmune haemolytic anemia, Sjögren’s syndrome and scleroderma. 

Now let’s zero in on the relationship between autoimmunity and gut health, starting with the role of leaky gut or intestinal hyper-permeability. I did a whole episode just on leaky gut on March 17, 2020, so you can check that out if you want to go super deep on this topic. There are several ways in which the gut can become permeable. First, you can have openings between the cells lining the intestines or the enterocytes, whose tight junctions hold them together, but also allow for them to open up and let nutrients and water through. When there’s dysfunction, they open too wide and for too long. This has been observed in celiac disease and gluten sensitivity in particular, but can also happen with other food sensitivities. The most common culprits are other grains that may be gluten free, in particular corn; pseudograins, including quinoa, amaranth, buckwheat and chia; diary; eggs; nuts; seeds; legumes (in particularly soy and peanuts) and nightshades (which are tomatoes, eggplants, potatoes and peppers). 

I believe that most of the more obscure food sensitivities are secondary to a gut infection, dysbiosis, stress, a poor or very repetitive diet or some other cause, although I have found that gluten, dairy and nightshades tend to be common primary causes. 

You can also have a permeable gut because a substance or infection causes direct damage to the enterocytes, or cells lining the intestines, which actually creates a hole in the lining of the intestines. This can come from certain foods containing lectins. There are two potentially harmful subclasses of lectins, called prolamins (found in grains, legumes and pseudo-grains, including quinoa, rice, peanuts and soy) and agglutinins (found in grains, pseudograins and nightshades). Legumes also contain saponins, another substance that can harm enterocytes. Keep in mind that even though there may be negatives associated with legumes (meaning beans, peas and lentils, but not including green beans, snow peas or sugar snap peas), overall they are super healthy foods with high fiber and the lectins and agglutinins found in them can be reduced by soaking, sprouting and fermenting.  They’re also deactivated by the heat during prolonged cooking, so if you do need to go off these foods for a time while healing your gut, you should eventually try to reintroduce them, if you’re cooking them properly. Some beans are worse than others, such as soy, peanuts and kidney beans, and the agglutinins found in them are more resistant to deactivation than others, so if you do have an autoimmune disease, you may want to steer clear of those ones forever, and the others until you are feeling better, and then slowly reintroduce a variety of legumes rather than focusing on one or two. 

Two other potential disruptors to proper digestion and mineral absorption that can cause a leaky gut are digestive enzyme inhibitors and phytic acid or phytates, which are both found in raw nuts and seeds, which is why when you have too many nuts you get that full, bloated sensation. If kept in low quantities, it’s fine. But if you really want to clean up your nuts, you can soak them in salty water then dehydrate them.

Finally, the more obvious and common culprits of damage to enterocytes in a standard Western diet are alcohol and synthetic food additives. 

An autoimmune paleo diet systematically eliminates these potentially problematic foods and then reintroduces them slowly so you can test your body’s reaction. While some people may need to eliminate these foods long-term, especially if they experience autoimmune symptoms when they’re reintroduced, many can be reintroduced in reasonable quantities in the context of a varied, healthy, whole-foods diet. 

Another potential cause of leaky gut is a gut infection causing damage to your intestinal lining. This includes parasites like Blastocystis hominis and giardia, as well as bacteria such as Yersinia enterocolitica, Helicobacter pylori, Klebsiella, Campylobacter, E. coli, an overgrowth of proteobacteria and Borrelia (the bacteria that causes Lyme disease). Gut tests like the GI Map, which I have many of my clients order, reveal most of these types of hidden infections and dysbiosis. 

Let me just mention that while many healthy people have Blastocystis hominis in their guts, there are two different types – the amoeboid form and the protozoa form. While the former is associated with chronic hives and adheres to the gut cells more, the latter is not, which may be one way to distinguish a Blastocystis hominis infection that should be treated versus one that can be left alone. 

Then SIBO or small intestine bacterial overgrowth, can be another cause of leaky gut. This can happen for a whole slew of reasons related to either low stomach acid or slow motility in your small intestine. However, a prior episode of food poisoning is one culprit that can lead to post-infectious IBS like I have, where you have elevated vinculin antibodies, which are tested using the ibssmart test. When you have that, you’ll likely have a lifelong struggle with SIBO, but it is manageable. 

And of course, invasive candidiasis can lead to intestinal permeability when the candida turn into their hyphal form and send tentacles out through the gut epithelium or lining. Note that we all have candida in our gut, but it can grow out of control due to a poor diet, stress and certain medications, including antibiotics. 

Speaking of stress, 80% of patients reported serious emotional stress before the onset of their autoimmune disease. Why would this be? Chronic stress leads to elevated cortisol levels. This leads to decreased digestive function, lower secretory IgA, which is your gut immune defense cells and elevated blood sugar. This opens you up to first gut infections, when your gut immunity is decreased, as well as poorly digested food, which has proteins that can trigger autoimmunity when they escape out of a leaky gut from a gut infection. 

Which gets us to the mechanism for autoimmunity. So when you have a hyper-permeable gut lining, and especially if you aren’t digesting your food well, which can be from a lack of digestive enzymes or hydrochloric acid from a variety of causes, undigested proteins will escape out into your system and trigger your immune system. When your immune system is triggered against certain proteins, it can also end up attacking similar proteins in your body. This is especially the case with gluten and Hashimoto’s thyroiditis, which I have, because the gliadin protein in gluten resembles the cells in your thyroid gland. However, studies have shown gluten to be an issue in many autoimmune diseases, and in creating intestinal permeability, so if you have any autoimmune disease, gluten is the first thing to eliminate for the long-term. 

Another contributing factor in Hashimoto’s and leaky gut can be a depletion of two key nutrients for gut health: l-glutamine, which is an amino acid, and zinc. Both are necessary for rebuilding the gut lining. They can often become depleted because of high stress, because they are also used in producing adrenal hormones. You’ll find zinc carnosine, the form especially good for the gut lining, as well as l-glutamine in leaky gut sealing powders like GI Benefits, which you can find in my Fullscript Dispensary. Before you go out and buy that, if you think you have a leaky gut, note that I generally don’t recommend using something like that until you’ve healed or while you’re healing SIBO, SIFO (aka small intestine fungal overgrowth) or other gut infections. 

Given it’s one of the most common autoimmune diseases and one I’m very familiar with, and because it has a special relationship with SIBO, I’ll just go a little deeper on Hashimoto’s, which is the cause of about 80% of the cases of hypothyroidism. First, it was found in one study that more than 50% of people with hypothyroidism had SIBO as well, because the slowing of your metabolism from being hypothyroid causes a slowing and stagnation in your intestines leading to bacterial overgrowths. This is often the case with constipation-related SIBO. But of course it can occur the other way around – where SIBO causes a leaky gut that leads to Hashimoto’s and hypothyroidism, as I already mentioned. Symptoms of hypothyroidism include constipation, pale dry skin, hair loss, muscle aches, weakness and tenderness, a goiter, a puffy face, brittle nails, excessive or prolonged menstrual bleeding, enlargement of the tongue, memory lapses, depression and joint pain and stiffness. If you have a TSH or thyroid stimulating hormone test and your level is above 2.0 (which is still within the standard reference range but not the optimal one) and you have any of those symptoms or symptoms of SIBO, I’d recommend asking for further testing including thyroglobulin antibodies and thyroid peroxidase antibodies to rule out Hashimoto’s. If you have SIBO, I’d recommend asking for your TSH to be checked because if your hypothyroid is caused by Hashimoto’s, then you can address it naturally, starting with gut healing and removing gluten and dairy from your diet, as well as testing and replenishing key nutrients. Left unchecked or just medicated with standard thyroid medications, which are important and necessary if you’re hypothyroid, Hashimoto’s will gradually destroy the thyroid gland, enlarging it and inflaming it. That was what my doctor told me would eventually happen to me in 2013 when I was first diagnosed. Happily, 9 years later, because I’ve done all the natural things I could to reverse the process of autoimmunity, my TSH levels remain normal and my antibodies have been normal for about 2 years now. 

Reversing Autoimmunity

Ok, now on to what to do if you have an autoimmune disease and want to try to put into remission and reverse as much as you can of the damage to your body. This is a brief summary, but I work with people to help them do this, so please reach out if you need some help. 

First, work to identify any food sensitivities using at minimum an elimination diet for 4 weeks of dairy, gluten, added sugar, artificial sweeteners (but stevia and monk fruit extract are ok), alcohol, processed foods, processed seed oils, soy and corn. If you have a very debilitating autoimmune disease, then I’d go full on a full autoimmune paleo diet (AIP) and also eliminate other grains, pseudograins, caffeine, nightshades, legumes, eggs, nuts and seeds, including spices derived from nightshades and seeds. There’s a specific way to eliminate and reintroduce foods on the AIP diet. Also, for some people, another helpful adjunct in decreasing immune activation and food sensitivities is proteolytic enzymes. One particular brand, Wobenzyme, has been studied and found to be particularly helpful in decreasing Hashimoto’s antibodies when taken in large doses on an empty stomach. 

Second, do stool testing or Organic Acids testing to determine whether you have any gut infections. Even if you’re not symptomatic, sometimes a combo of different gut pathogens combine to mean you have neither diarrhea nor constipation but you may still have an issue that’s causing inflammation and a leaky gut. Of course, if you have any gut symptoms, then that’s definitely a likely factor. Usually herbal antimicrobials, probiotics, prebiotics and polyphenols, through diet or supplements and digestive supports like Betaine HCl to replace low stomach acid, pancreatic enzymes or bile support may be needed, depending on what is found on your tests. 

If nothing comes up in your gut testing, you may need to be tested for other viruses like Epstein-Barre to see if there’s been a reactivation there, so you may need some antiviral support. 

Third, after gut infections are dealt with, a gut sealing and healing supplement is helpful in sealing up a leaky gut and rebuilding the gut lining. 

Fourth, you may need to test for and address nutrient deficiencies of key nutrients like vitamin D, omega 3 fatty acids, B vitamins, selenium, zinc and magnesium, which can also be a factor in autoimmunity, or at minimum take a multivitamin, fish oil and any other nutrients that show up as deficient on an Organic Acids Test. Testing for nutrient deficiencies and supplementing where necessary gives your body the tools it needs to modulate your immune response, fight bacteria and viruses and support an appropriate inflammatory response.     

Fifth, another factor that can often impede healing is a congested liver that is overloaded dealing with toxins, which can be identified on an Organic Acids Test. If you find this, there are certain supplements that are recommended to support your liver in detoxifying your body. In initial interviews, I also ask people about signs of potential heavy metal toxicity and mold exposure. But other basics like making sure your water is pure and you’ve eliminated toxins in your personal care products, cookware and food is important in decreasing the burden on your liver. 

Sixth, since stress is so intertwined with autoimmunity, finding and addressing causes of stress, and managing unchangeable causes is an important step. This may involve starting therapy, ending toxic relationships, leaving a stressful job, or a program of meditation, mindfulness, prayer, yoga or breathwork

Finally, and probably the most important step, is persistence. Reversing autoimmune disease doesn’t happen overnight. It takes long-term persistence and commitment to yourself and caring for your health. I was diagnosed with Hashimoto’s in 2013 but didn’t see my antibodies normalize completely until a couple of years ago, so it took patience to eliminate foods and change my diet, clean out my liver, stabilize my nutrients, work on my gut health issues until they were truly under control and then stick with all those positive changes over time. Of course, the rewards are great if you can persist.

If you’re struggling with from an autoimmune disease, you’re welcome to set up a free, 30-minute breakthrough session with me (Lindsey). We’ll talk about what you’ve been going through and I’ll tell you about my gut health coaching 5-appointment program in which I recommend lab tests, educate you on what the results mean and the protocols used by doctors to fix the problems revealed. Or if you’re ready to jump in right away or can just afford one appointment at a time, you can set up an 1-hour consultation with me.

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