The Autoimmune Solution Pillar II: Get Rid of Gluten, Grains, and Legumes

February 20th, 2015

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The Autoimmune Solution Pillar II: Get Rid of Gluten, Grains, and Legumes

The Autoimmune Solution Pillar II: Get Rid of Gluten, Grains, and Legumes

In The Autoimmune Solution, I walk you through the four pillars of my protocol for preventing and reversing autoimmune disease. This is part two of a four-part series on each pillar. Read the other parts here:

Pillar I: Heal your gut.

Pillar II: Get rid of gluten, grains, and legumes.

Pillar III: Tame the toxins.

Pillar IV: Heal your infections and relieve your stress.


Last week I explained how having a leaky gut puts you firmly on the autoimmune spectrum. That’s why “Heal Your Gut” is the first pillar of The Myers Way®. Now it’s time to make some changes that will get your gut back to a state of health. One of the biggest ways you can do that is to stop eating foods that are causing further inflammation and damage to your intestinal tract.


What is Gluten?

Gluten is a group of proteins found in grains like wheat, semolina, spelt, rye, kamut, and barley. It’s what gives bread its sticky, doughy texture, but that’s not the only place you’ll encounter it: gluten is used as a food additive in practically every processed food, from salad dressing to ketchup.

You may be wondering how something so mainstream could be harmful to your gut. Wouldn’t we all be sick? Well, unfortunately, it has become mainstream to have a chronic illness such as heart disease, cancer, or an autoimmune disease–and the rates are rising. Gluten has been linked to more than 55 diseases, and an estimated 99% of people who have either celiac or non-celiac gluten sensitivity are never diagnosed.


How does gluten cause leaky gut?

In The Autoimmune Solution, I explain in great detail how gluten contributes to a leaky gut which then leads you down the path to autoimmune disease. It prompts your immune system to attack your own tissues, it’s not easily digested, and it contributes to gut imbalances like Candida overgrowth and SIBO. But even more damaging is gluten’s ability to trigger the body to produce zonulin, a protein that can signal the tight junctions between the cells in your intestines to open and stay open.


The problem with grains and legumes

Wheat is not unique. Other grains, pseudograins (like quinoa), and legumes contain similar proteins that contribute to leaky gut in several ways:

  • by damaging intestinal cells
  • by opening the tight junctions of the gut lining
  • by feeding unfriendly bacteria to create gut dysbiosis

The edible portion of these plants is the seed, which contains the embryo. In order to pass on its genes, a plant produces its own chemicals to repel pests and prevent digestion. These chemicals can be very damaging to someone with an autoimmune disease. I outline all of these in The Autoimmune Solution in much greater detail, but I want to highlight a few in particular:

Lectins are plant proteins that bind to carbohydrates. The two types of lectins in particular that are known to cause a problem in humans are agglutinins and prolamins.

Agglutinins function as a natural insecticide and can be an aggravating factor in autoimmune disease. The effects of lectins within our bodies can be subtle and hard to recognize, but some agglutinins are incredibly dangerous. Ricin, a lectin in castor beans, is fatally toxic, even in very small amounts.

This is why genetically modified organism (GMO) grains are especially harmful to those of us with autoimmunity. They have been engineered to produce more of their natural insecticides–the very chemicals that are so inflammatory! Because of this, if you do choose to include grains in your diet, I’d recommend going for non-GMO and heirloom varieties.

Prolamins are necessary proteins for seed growth, and therefore they are not easily digested. Gluten is a prolamin, and most grains contain a prolamin similar in structure to gluten. In a process called cross-reactivity, those prolamins can cause a similar immune response in those who are sensitive to gluten.

Phytates and phytic acid inhibit digestion and binds to certain minerals (specifically zinc, iron, and calcium) which are vital for our immune system to function properly, preventing their absorption. GMO grains contain an even greater concentration of phytic acid.

Saponins called “glycoalkaloids,” found in very high levels in pseudograins and legumes, are also a natural insecticide produced by these plants. Once they escape your gut lining (which is easy to do if you have a leaky gut!), they enter the bloodstream and destroy red blood cells.


Other foods to toss

I also recommend that those with autoimmune diseases avoid vegetables in the nightshade family (Solanaceae), which includes tomatoes, peppers, and potatoes. These plants are very high in lectins that damage the gut lining, easily enter the bloodstream, and do not break down in cooking.

Just as a seed (plant embryo) protects itself naturally with chemical defenses, so do other embryos, like eggs. Just like a seed, eggs contain a protective enzyme. The enzyme, called lysozyme, is inflammatory to people with autoimmune conditions.

While you’re going through the 30-day program in The Autoimmune Solution, there will be many foods you will avoid temporarily and then add back in. Grains, pseudograins, legumes, and a few other foods will probably need to stay out of your diet for good, as so many people with autoimmunity are extremely sensitive to them. Gluten is an absolute “no no,” I don’t recommend that anyone add gluten back into their diet.


A note for vegetarians

You may be reading this wondering what in the world you’re going to eat if your diet is one that relies on rice and beans. I became a vegetarian at 14, and it was very hard for me to see that my seemingly healthy diet was causing more problems for me–I share my own health story in The Autoimmune Solution, and the path I took to finally getting better. The good news is, there are plenty of vegetables that you can continue to enjoy while going through The Myers Way®. My nutritionist and I put together pages and pages of recipes as well as a seafood meal plan in The Autoimmune Solution to help you make the transition away from gluten, grains, and legumes toward a diet that heals you.


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  • Patty

    What are your thoughts on corn or non GMO corn chips for a taco salad? I haven’t seen corn called out specfically. Is it OK to have a limited amount (1/2 cup)? Does corn have the same issues as wheat and gluten?

    • Karen

      From what I understand, corn is full of mold and is not a great food for those with autoimmunity. What do you think, Amy?

      • I agree– there are lots of reasons it’s bad for people with autoimmunity!

    • Tammy

      I know corn and soy are the worst for being GMO.

      • Yes, it’s almost impossible to guarantee that corn or soy are nonGMO because of cross contamination.

    • Corn is a big problem for people with autoimmunity. First off, it’s a grain. Second, it’s almost ALWAYS genetically modified. I’d recommend avoiding it, at least for a few weeks, and see how you feel. Here’s an article I wrote specifically about corn:

  • julie1939

    My latest challenge is diabetes. I eat beans to help control blood sugar. So I am very dismayed to hear that they cause inflammation. I have been mostly off grains, sugar, and dairy for more than 20 years. I have read much of your book and attended the Autoimmune Summit. Thank you so much for your tremendous efforts.
    Do you have a suggestion for lowering blood sugar? I don’t know why I recently developed blood sugar problems, since nobody in my family has it.

    • Chelsey Vuyk

      I have been using and teaching others how to use essential oils for many different things, blood sugar control being one of them. Cinnamon essential oil works WONDERS. There’s an oil by doTERRA that many people use, including those with diabetes, called Slim and Sassy. it not only helps your body control blood sugar, it also aids your body with healthy digestion, cleansing, and it gives me a great boost of energy. it contains peppermint, cinnamon, lemon, grapefruit, and ginger essential oils. I’d be happy to send you some to try and see if it can be a solution! If you’re able to take some internally and then test your blood sugar about 10 minutes after, oh and test prior to taking to see the difference, you’ll know very quick if it works well for your body.

      • Carol van der Schaar

        I thought it was unsafe to use essential oils internally

        • Chelsey Vuyk

          that is true for almost all brands of essential oils. Have you ever used or heard of doTERRA essential oils? they are HUGE here in Utah, I’ve been using them for almost 4 years now and I teach other people, mostly other mom’s, how to use them safely. Its my passion now. I got into them because of their sourcing practices, I spent a lot of time researching and learning about them, these ones take the cake by, well, seriously nothing else can even come close to the purity and potency of them. They are amazing. If you want to send me an email I can send you some info you can look into yourself (at least that’s what I like to do, I’m not very good at taking people’s word for it) my email is [email protected]

    • These are general recommendations for people with autoimmunity and it does vary from person to person. Have you considered setting up a consultation with my dietitian? She would be able to formulate a plan that is more specific to you as an individual!

      • julie1939

        Thank you for your reply. I have tweeked my diet so much for so long that I doubt that a dietician could be helpful. I have studied nutrition a great amount. I think that some lab testing would be better, but finances aren’t great right now. I seem to get weird stuff, like my thyroid became very painful. That was 25 years ago. There is a lot of fatigue and depression now, even though I am pre-diabetic. I have looked at the list of functional medicine doctors in this area, (Chicago area). Almost none are MD’s. I was hoping that some lab work would be covered by Medicare. I don’t want to control diabetes; I want to not have it.

    • kim

      I have read that to much bad fat coats your cells so the glucose then can not get in and then just floats around in the body or blood stream causing a sugar rise. My advise is to clean up your diet. No processed foods or snacks. Lots of healthy veggies at least a pound or 1/2 cooked and raw, organic grassfed cage free meats and eggs if your don’t have a problem. Berries in moderation. Chocolate of 85 percent or higher. Dr. Medical has a great 85 percent bar with only 2 grams of sugar. Be clean and eat only very healthy fats, these will help you. Avocado and coconut are great. Hope this helps. Beans have high carbohydrates, so potentially if eaten to much may turn into sugars again not helping anyone’s cause, also can be trouble some with nutrient absorbtion if you don’t soak the beans or sprout them.

      • julie1939

        Dear Kim, Thank you for your response to my post to Dr. Amy Myers. It brought tears, because I feel alone and frustrated with the diabetes. I have always eaten healthy. I have been off grains, sugar, and dairy for 20 years and nobody in my family has diabetes. My frustration is mostly: why did I do all the preventative stuff and got it anyway? I attended the autoimmune summit and the diabetes summit. I just keep hearing “Eat right and you will reverse it, etc.” I guess I am thanking you in the wrong way.

        I study nutrition non-stop. None of the herbal stuff has helped. You mentioned sprouting the beans. What do you do with them after sprouting? Do you cook them after sprouting? Beans is the only thing that has helped my blood sugar. My mantra for eating is the 3 S’s: soup, smoothie, stir fry (which is steaming). My digestive system doesn’t handle very much raw vegetables.

        I attended the diabetes summit, but missed maybe 6 speakers. I am hoping to find something helpful by visiting their websites. I have been doing things for detox and fixing the gut. The only thing I’ve found helpful right now, is the suggestion to do more aerobic type exercise. I have been doing mostly resistance exercise.

        I will try some essential oils, but don’t have the belief that they will reverse the disease. I am stopping eating most fruit. Perhaps I can get my MD to do some lab testing, more than A1C and glucose. My insurance would not cover a functional medicine doctor, so I would need to believe he/she would help. My blood sugar is not terrible, but I don’t want to be diabetic. Thanks again. Julie

        • kim

          The bean can be soaked and eaten raw or eaten cooked. You can buy sprouted lentils and make lentil soup and put lots of veggies and chicken, vegetable, or mushroom broth. Its important to heal the gut, lots of homemade bone broth is good too. Cook your veggies then and eat lots of raw fermented veggies and coconut water, these are very healing to your body. But ultimately you have to listen to your body.Donna Gates also knows her stuff and I take some of her multi packs.

          Also I used to be a raw vegan, and I know a couple of people that were totally cured when they ate the raw diet and juiced greens. Brian Clement has a utube video on this and you could watch it. This diet is hard to stay on because you literally only eat veggies, juices, wheatgrass, and sprouted beans.

          I know you must be frustrated but hang in there. You have to find things that work for you. No processed ot high glycemic loads would be good for you.

          Also what I find is what works for one doesn’t always work for another.

  • Mandy

    Getting off dairy was way more important than getting off grains, for me personally. I had a food sensitivity test done and was very sensitive to dairy (and also a little bit to eggs), but not at all sensitive to gluten. I do still eat some gluten, but it’s always organic and either sprouted or fermented, which seems to help. And organic sprouted grains don’t seem to bother me too much either. I also don’t eat meat for ethical reasons (and never will). Plus, there are plenty of reputable peer reviewed studies (i.e. Dr. Campbell and The China Study) that show that animal protein causes many other health problems.

    • If you’re going to eat grains, organic and sprouted are the way to do it! I respect ethical choices to avoid meat and find some people do well that way. Dairy, as you said, is a big problem for a lot of people–I take my patients off of it.

  • New Urbaneer

    Not all seeds, and their inner bits, are created equal. I just healed my leaky gut with flax flour. I ground up 2 heaping Tablespoons of flax seeds and drank it with water every morning for a few weeks and ouila, my formerly leaky gut leaks no more!
    I’m adding back good bugs with my own tasty water kefir and bob’s your uncle

    • New Urbaneer

      Oh, and I forgot, I’ve been adding back eggs slowly but surely, and hummus doesn’t cause any problems and never has. Lentil rice is ok once in a awhile and I plan to continue adding that back in larger quantities.
      In fact, I have even had the wonderful experience of eating a tomato again. I got carried away and ate more than I should have so I have to cutback on that for awhile, again, but I see no reason why I shouldn’t go about treating my food sensitivities just like the allergists treat incredibly serious allergies by adding them back in very slowly and only a little bit at a time.

      I am going to stay off gluten for awhile but I will be trying teff before the 6 months are up. I think you overly sensitize the body when you eliminate all traces. It’s like when you quit smoking, your body get’s too sensitive to the smell of smoke unless you do smell a little second hand now and then.

      • Yes, I treat my patients with an elimination diet where they take several foods out and then add them back in. After their guts have been healed, most people can tolerate small quantities of these foods again–but for a lot of people with complex autoimmune diseases, I’ve found they remain sensitive to grains. I would never recommend adding gluten back into the diet because of its ability to encourage the release of zonulin in the GI tract. Also, it doesn’t add anything (nutritionally speaking) to your diet. But in the end–if foods like hummus and rice work for you, that’s great!

  • DP2008

    I appreciate your hard work behind your dedicated mission in life to save ppl from auto immune diseases thru auto immune solution. Rice and wheat and all grains are made by nature for feeding the birds’ digestive system and NOT ours and that we would get diseases if we would eat them. But man has lived survived with and without peace of health for more than 5000 yrs past! A good food that suits the human system will not bring ill health in the short or long run!!
    What food was meant for mankind is still an argument. My nature wrote only raw diets are meant for mankind, & he showed practically curing brain cancer to elephant foots and leprosy tho it took more than 6months on raw diet.
    I believe legumes need a better treatment under your brilliant third eye analysis! I say Not all beans are dismissable. Kidney beans, edamame, soya beans, are causing stomach ache to the eaters! Also they are high proteins , not required by human body!
    Sprouting removes the phytic acid

  • Scott

    Have you seen a reversal in non diabetic peripheral neuropathy with this diet? I’ve gone gluten free for 5 weeks and reduced sugar intake by 90%. Sadly no change. Nortyriptolin has not helped either.

  • cb

    where do we find the answers to these questions?

  • Lauren

    Are paprika and cayenne pepper allowed after the 30 days? I can’t figure out if they’re on the bad list because of a connection to nightshades, or another reason. Thanks! I’m on day 9… 🙂

    • Hi Lauren! Paprika and cayenne are nightshades, so if you’re going to try them after the 30 days make sure you follow my food reintroduction protocol so you can gauge any reaction you might have.

      • Lauren

        Will do – thank you!

  • Danika Stokes

    Hi there. I have a few questions for you Dr. Myers. I have had lupus for 22 years, and over the years I’ve acquired several other autoimmune diseases. I have been around the country, literally, seeing different alternative doctors. But in the past 2 years I’ve really started focusing on my gut. 14 months ago, I woke up with a rash that you can’t fathom, on my face. I didnt’ leave my house for 4 months. Perioral dermatitis was the diagnosis, worse case Stanford has ever seen. Because of the lupus diagnosis, I couldn’t take the drug they would prescribe, nor did I want to. So I embarked on the GAPS diet, very strict for 4 months, rash almost gone. I eased up on it a bit and it’s still around a bit…enough to know it’s not gone. This GAPS diet let me to do a Candida cleanse, which led me to Underground wellness, which led me to join Gut Thrive with Sean and Christa. However, in the midst of it all, I had 23 and me done and I found out I’m homozygous for MTHFR C667T. Not good! I am currently working with Dr. Mullan and Yasko in regards to my mutations. So, that was a very quick summary of 22 years…my question, where does this fit in to the time line of healing? I have been off gluten, dairy and sugar for 14 months (still having low sugar fruit) and have been able to get off two of my three meds, only 5 mg of prednisone left to go. But I’m a little stumped on where to go from here. I haven’t heard you mention mutations, but I’m assuming this is my first stop, getting those working? I know I have a fungus, parasite and bacteria but I don’t feel like I can deal with that until I am methylating…can you give me a brief order of steps when a person has gene mutations like this? Thank you so much!

    • Hi Danika, my first suggestion would be to read my book, The Autoimmune Solution. I do talk about MTHFR mutations, and that’s something I see a LOT of in my clinic. You can still go through the 4 pillars of my program while you are addressing the MTHFR, and I would highly recommend it! Other than that, I would say that you should set up a consultation with me or my registered dietitian so we can help you get a plan!

      • Danika Stokes

        Thank you for your response a few weeks ago! I’m waiting for your book in the mail but I have a few questions. You mentioned I could get a consolation with you to get a plan in place but I was wondering if that would still work if I’m working with Dr. Mullan and Dr. Yasko in regards to my methylation issues. They are only addressing those issues so I’m looking to find someone who can oversee my plan in its entirety. I started the supplements a week ago to get methylation started and I feel lousy, I think I may have started to fast. So I’ve backed off. And will start up again when I’m feeling better. I’m feeling very discouraged at this point. Do you see people improve even though they’ve been sick for years? I’ve had lupus for 22 years and since then have so many other health issues. At times I feel like I’m too sick to turn it all around….
        I’ve already invested my time and money into working with Yasko and Mullan but I feel like I need a doctor to work on all the other aspects, would you let me know if you’d be open to this? Thank you so much .

        • Danika Stokes

          Hi Dr. Myers,
          I just spoke with your office. Sadly, your next appointment is not until December. What do you advise for people who need your help? I sadly got my labs back this morning and my platelet count is at 4,000. Clearly this level is very serious, I’m working on my mutations and am working on getting on your diet (which i’m not that far off anyway). I wanted to know how I can do this alone? I ordered your book, will read that thoroughly. But I’m just so discouraged, I’m at the point where there doesn’t seem to be much help out there. Lots of great info, but few to help with the supplements and lab ordering and really tailoring things to an individual. I understand what it takes to slow down/reverse disease, but with these levels I don’t feel like time is in my favor. Thanks for your thoughts.

          • Hi Danika, yes I have seen people improve after years and years of being sick. But it does take a long time to turn the Titanic around! I am booking far out right now, but my clinic is looking to bring on a second physician which will hopefully cut that wait list in half. I highly recommend getting a spot on my schedule regardless, and then in the meantime maybe finding a functional medicine practitioner closer to you? You can search for a doctor like me here:

          • I wish you the best in health and I hope you start feeling better soon!!

  • Natural Neda

    Where can I find on your site when reintroducing some of these foods back in?

  • Sylvia

    Is it ok to consume xanthum gum? I have sjogrens syndrome and it is recommended for increased saliva production. I have noticed it as an ingredient in many gluten free

    • As with any food additive it could cause reactions in some people, but it really depends

    • kim

      I would like to know more on this too as my coconut cream I eat from Trader Joe’s have xanthum gum in it.

  • Sam

    What to eat when you are a vegetarian? Is there any problem with gluten free grain like oats ,buckwheat, millet ?

    • Yes, that is the subject of this article–all grains and pseudograins can cause problems in people with autoimmunity

  • Maryann McGrath

    Dr. Myers, is it okay to have a handful of cashews or almonds once in a while. I have Celiac Disease and right now my systems seem to be in check. I’m currently, gluten, dairy, grain, soy and corn free. I have eggs 3xs times a week and I’d like to have nuts here and there. Is it okay provided I’m feeling well to continue with both the eggs and the nuts?

    • If you introduce them and do fine with them I don’t see why not, I would just not overdo it.

  • Lisa

    I am a patient of a doctor who practices functional medicine. He follows your philosophy and I am now going to buy your book and try a 30 day elimination. I know it will take a lot of will power, but I want to heal my body. I was diagnosed with progressive Inclusion Body Myositis which there seems to be no cure for. For the last four years I have tried to be proactive. I have been drinking green smoothies for four years as well as detox drinks with apple cider vinegar, lemon and coconut water. I exercise, pray, and try to meditate whenever I can. I have always eaten well and stayed about 90% gluten and dairy free as well as minimal grains. I was tested and found to have two markers for gluten intolerance.I know you say it is possible to cure or reverse auto immune diseases. I pray that this will give me a chance to heal. I want to believe that just because there is no medical cure for what I have, I can still turn this illness around! Thank you for sharing!

    • You’re welcome, Lisa! I wish you the best of health!

  • Lisa

    Hi, I just posted a message that ended up about 16 messages down by people that sent messages about a month ago! :(. Not sure what happened there….just hoping you see my message!

  • Cheryl James

    In my grandparent’s day autoimmune disorders were unheard of. My theory is that the food here in the US is making us sick. I have several autoimmune disorders and eat only organic, homemade foods, use organic personal care products, organic household products etc. and I seem to be doing better. My labs show no inflammation. I’m not cured but I feel better, have less flares since I’ve been eating this way and I’m gluten free and mostly dairy free. What are your thoughts on mainstream food, fast foods etc making us ill?

  • Chris

    I am reading your book right now and excited to get started. Where is the list of foods that can be tried after the 30 days to see if one can tolerate?

  • Perley Peters

    If you can’t find fresh wild salmon can we use canned wild salmon?

  • Carol

    I have been on The Myers Way for almost 2 months now. I’ve seen some improvement but not the miraculous reversal I was looking for. Lost quite a bit of weight, but still have my aches and pains. And I find that I’m having a hard time eating so much meat, especially at breakfast. I used to make protein shakes for breakfast made from organic vegan protein (peas and rice) but that’s not allowed on your diet. Is there another type of protein shake that would be acceptable? What about chlorella? Do you know anything about that? I don’t want to give up the diet, but it seems rather assiduous. Any advice?

    • Some people are able to add protein powder back into their diet, so you may be able to tolerate it! My recommendation would be to set up a Wellness Coaching session with my registered dietitian who can give some more tailored guidance to go along with the book.

  • Jessertel

    Dr. Myers,
    What is your recommendation for individuals who do not feel relief after completing the 30 day trial? I eliminated everything without exception and even started some of the supplements, but I still have very clear symptoms (nausea, bloating/stomach inflammation). I was diagnosed with IBD in Jan after 5 years of stomach problems and put on mesalamine. I’ve been off gluten, grain and dairy for 2 years now… what’s the next step??