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The Problem with Grains and Legumes

June 12th, 2019

the problem with grains and legumesProminently situated at the base of the food pyramid, grains are promoted as the fiber-rich foundation of a healthy diet. But are grains really a necessary part of your diet, or can they in fact be harmful?

If you have an autoimmune disease, you may already be aware of the fact that gluten, the protein in wheat that gives bread its sticky, doughy texture, is an inflammatory substance. However, wheat is not unique. Many of the plants that we consume contain similar proteins that will increase inflammation in your body and contribute to a leaky gut. Although most people benefit from avoiding foods such as grains, pseudograins, legumes, and nightshades, I recommend for those with an autoimmune disease to omit these foods from their diets, at least until their inflammation has subsided and their gut has healed. The Myers Way Comprehensive Elimination Diet is the best course of action to determine whether or not these foods will be a problem in the future.

In order to better understand the potential harmful effects that they can have on your body, it is first necessary to understand the function of grains, pseudograins, and legumes in terms of plant biology.

What are grains, pseudograins, and legumes?

The grains that we eat are the seeds of the Poaceae family of grasses, commonly called cereal grains or cereal grasses. This family includes, among others, wheat, barley, rye, corn, millet, oats, sorghum, spelt, teff, rice, and wild rice.

Pseudograins are the seeds of broadleaf plants (non-grasses) that are used in the same way as grains. They are often promoted as gluten-free alternatives, and examples include quinoa, buckwheat, amaranth, and chia seeds.

Legumes are plants in the Fabaceae or pea family. The part that we eat is the bean or pea (the seed) and sometimes the pod as well. This family includes beans, clover, alfalfa, lentils, peanuts, chickpeas, lima beans, soybeans, and others.

The edible portion of these plants is the seed, which contains the embryo. A plant’s mission is to pass on its genes, and because a plant can’t move around, it relies upon animals to spread its seeds about. A seed, therefore, is designed to withstand digestion, moving through the body in order to be “planted” on different soil. There are several properties of a seed that allow it to survive the gastrointestinal tracts of the animals upon which it depends, all with potential to cause harm and an inflammatory response.

Why should you avoid these foods if you have an autoimmune disease? Here are some key reasons:

Certain chemicals within these foods make them inflammatory in our bodies.


Lectins are plant proteins that bind to carbohydrates. There are many different types of lectins, and not all of them are harmful. 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. For example, Ricin, a lectin found in castor beans, is fatally toxic to humans even in very small amounts.

Genetically modified organism (GMO) grains are especially harmful when it comes to agglutinins. They have been engineered to produce more of their natural insecticides, which may give us a heartier crop, but one that is more 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. For example, orzenin in rice or avenin in oats. Prolamins contribute to the cross-reactivity experienced by so many with a gluten sensitivity, and yet grains that contain them are often used as gluten-free alternatives.

Those with autoimmune diseases should also 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.

Phytates and Phytic Acid

Phytates and phytic acid occur naturally within the seeds of grains as a phosphorus store. Phytic acid inhibits digestion and binds to certain minerals (specifically zinc, iron, and calcium) which are vital for our immune system to function properly, preventing their absorption. Usually a small amount of phytates in your diet would not present a major problem, as long as you were getting adequate nutrients from the rest of your food. But when grains are the basis of your diet, mineral deficiencies can result.

Again, GMO comes into play. GMO grains contain a greater concentration of phytic acid, and heirloom grains are a safer bet, should you choose to include them. You can break down some of the phytic acid in grains by slow cooking them, sprouting them, or soaking them overnight in water mixed with a little bit of lemon juice or apple cider vinegar. These methods activate phytase, an enzyme present in the plant that breaks down phytates. However, if grains are a major part of your diet they can still prevent digestion and contribute to a leaky gut.

Foods (like seeds) that are not easily broken down strain the digestive system.

When you eat, your body produces enzymes to break down proteins into individual amino acids. However, inhibited by the chemicals within a seed, the enzymes are unable to perform this essential task, causing a chain reaction. Your body then produces more enzymes, and in this process the body’s nutrients are used while not getting any in return. Worse still, an overabundance of digestive enzymes in the gut will wear down the gut lining and contribute to a leaky gut.

Undigested and partially digested food in the gut leads to bacterial overgrowth.

An overabundance of partially digested food in the intestinal tract provides food for bacteria. A healthy balance of good bacteria is essential for your body’s overall well being, and because some bacteria will feed on partially digested grains, and others won’t, it’s easy for an imbalance to occur. Bacterial overgrowth can lead to a wide array of problems and can even help to break down the gut lining.

Undigested grains, pseudograins, and legumes contribute to a leaky gut.

The gut is by design slightly permeable. The ability for some substances to pass through the gut lining is an essential function of our bodies, allowing us to absorb nutrients from our food, fight infection, and assemble the proteins and enzymes that are necessary for life. However, the gut can become hyperpermeable, and this can lead to autoimmunity.

Because they aren’t completely digested, grains, pseudograins, and legumes pass through the gut barrier intact. This helps to increase the permeability of the gut barrier a) by damaging the cells that line the gut and b) by causing an inflammatory response once outside the gut. A cycle then begins where the body responds to the grain particles with inflammation, which then damages the gut lining, which in turn becomes even more permeable, allowing more undigested food, toxins, and bacteria to leak out. Your body can confuse these foreign “invaders” with your own tissues – a process known as molecular mimicry. Soon, the immune response gets out of control and begins to affect more tissues and systems within the body, and autoimmunity results.

When it comes to nutrition, quality is key.

Grains, pseudograins, and legumes are not nutrient-dense foods, and they can actually prevent you from absorbing the amino acids you need for a healthy immune system. Even grain varieties that are promoted as wheat-free alternatives are just as devoid of nutrients. It is much better to replace these inflammatory foods with healthier choices such as sweet potato, squash, and dark leafy greens.

Modern day grains have been bred so that they no longer resemble the grains that our ancestors consumed, so if you do choose to include grains, pseudograins, and legumes in your diet, opt for non-GMO, heirloom varieties whenever possible (and make sure to soak, sprout and slow cook them). Try not to make them the focus of your diet. Those with autoimmune diseases would be wise to omit grains, pseudograins, legumes and nightshades completely, and to avoid nuts and seeds as well, which for many of the same reasons can be inflammatory. Once you have healed your gut, reduced or eliminated your medications and are symptom free you may be able to indulge in these foods every once in a while.

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17 Responses

  1. Carey Huyser says:

    What a great summary! I have been searching for something this comprehensive, and here it is. Just sent this link to my parents.

  2. bRAD says:

    As I was reading this I was wondering about non-grain nuts and seeds (almonds, cashews, sunflower and pumpkin seeds, etc.), then you briefly mentioned them in the last paragraph. Are these equally inflammatory and in the same ways as the grain, pseudograins, and legumes?

    • Vanessa Bradshaw-Jones says:

      Almonds, cashews and other seeds also need to be soaked prior to eating them, because they contain phytic acid and other inhibitors as well. So yes, they are pro inflammatory and has to be consumed in small amounts very seldom if you suffer from autoimmune disease

  3. DocMB says:

    This explains a lot to me about why I am still suffering from acid reflux that makes me unable to sing and why I have had such a hard time losing weight. In the past four years, I have eliminated so many things from my diet due to new and suspected food allergies that I have lost 50 pounds. I work out 6 days a week for 1 1/2 – 2 hours, eat very healthy foods (three meals and two fruit snacks a day), and still need to lose more weight. It was like my weight would not budge even with all of the effort (I thought it was age and a slow metabolism which it still may be to some degree), but my singing voice seemed permanently gone which depressed me because I do it well and make a living with it.

    I have been to an ENT who cleared me of having any nodules, etc, but said I have minor irritation at the esophagus from acid reflux which shocked me because I don’t have bad symptoms like my mother does. I do have severe allergies though and always have since childhood. I am so bad that I joke that I am allergic to everything under the sun and I really am allergic to everything under the sun.

    My internist wanted to put me on Synthroid (for minor thyroid issue) and he wanted to put me on Omeprazole both of which I refused. If I can avoid being medicine I will do it. I am a good patient and I have always tried to live a healthy lifestyle even as a former athlete. I prefer to work with my body as opposed to feeding it medicine constantly. It is bad enough that I have to keep antihistamines nearby just in case.
    I really believe that the foods we eat are at the root of most of our societal illnesses. I am so allergic to the environment and animals that my allergist was shocked at my test results. I had to get six allergy shots a week at first and my arms were bruised.

    Fed up with doctor’s assumptions that I am just a fat, lazy, couch potato (which I have never been-one doctor tenderly explained that I can take fewer trips to the buffet table-which I never do anyway but my skinny friends do), I did my own research on food, allergies and obesity, eliminated some foods I suspected were making me sick, and added a few amino acids and vitamin supplements to my diet. I was already allergic to milk products (as are many African Americans and people with Mediterranean backgrounds) and eliminated wheat-gluten, corn, eggs, and soy from my diet. I replaced rice and soy milk with almond milk which I rarely use anyway. I cook with coconut and olive oil on occasion. I sadly had to give up tacos (corn) and flour tortillas.

    When I did these things all of my crazy symptoms that I had been experiencing (and that my doctors could not help me with but wanted to prescribe medicine for or put in a useless splint) went ALMOST completely away. No medicine. No surgery. No starvation diet. The carpal tunnel syndrome that surfaced during my pregnancy that they said would go away up to six months after childbirth finally went away after 6 years of discomfort and useless splints. My harmless thyroid cysts decreased. I slowly began to lose weight but not enough. The mood swings, daily headaches, achy joints and feet, nasal congestion, runny nose and sinus infections subsided. No more antibiotics. The hiccups, unusually full feeling at the top of my stomach, seemingly random and scary burping events, eczema, swollen eyes and lips went completely away. I felt more whole again. I was not scared to eat foods. I just did not eat what I discovered irritated my stomach and my body. I take antihistamines with less frequency but they are still very necessary for me right now since I have so many environmental allergies (and I do not want to stay cooped up in the house to avoid mother earth and all of her glory). ;-)

    I was already eating what I thought were healthy foods so my vitals were really, really good to have been so overweight (264 pounds at the time). I might add that my body frame is medium-large. I am naturally muscular and being an athlete for so many years added to it. My thighs are naturally large. My butt is big. My waist is small. My boobs are big. I have a voluptuous hourglass figure. I will never be 110 pounds. My healthy weight goal is 140 pounds. Anything less than 135 would make me anorexic. I am currently 214 pounds. I am 5′ 6″. People-learn to love yourself.

    To continue…My doctors said my vitals were better than their own vitals, but neither they or I could not explain why some of the gastric and joint symptoms I experienced remained even after I eliminated some of the top allergens from my diet. As a matter of fact, my doctor does not even know that I have lost so much weight because I have not been back for my annual check up yet. He was elated to see that I lost 24 pounds. He will be over the moon to hear that I am even smaller. I can’t wait to discuss what I have discovered.

    And now I know it is probably the grains and legumes I think are healthy for me that are causing my body to fight itself, to keep weight on and that are making my esophagus render my voice to a raspy, hoarse mess. I am eating “healthy” foods that are not healthy for me. I honestly do not know what I am going to do because I love to eat so many things that my body apparently hates. I do not know if a food allergy test will even work for me since I have gone without certain foods for so many years now, but one day I will get tested. I just feel that my body has told me since I was a child what it likes and does not like and all of the Pepto Bismol and Omeprazole in the world won’t deal with the real issue that causes the problems so many of us face. I don’t want to be on any kind of medicine for the rest of my life.

    I eat a ton of rice, bell peppers, beans, peas, gluten free oats and occasionally some
    gluten-free processed cookies with buckwheat in them and I lose my voice
    every time reintroduce one of these back into my diet. I haven’t narrowed it down, but I am getting close. Alfalfa makes me throw up immediately. I am allergic to grass. Why wouldn’t I be allergic to other edible grains/grasses, etc.? It makes perfect sense to me even without the thorough examination and food sensitivities test. I have to learn more about the other names these foods are labeled under as well. It is not so obvious for those of us who are just learning.

    But I have learned so much. I am continuing to learn that the ingredients I may be allergic to are in everything (food, soaps, shampoos, vitamins, etc.) and they all have different names. That is why I believe once I figure out the rest all of my symptoms will go away completely.

    Thank you for sharing what you know with inquiring minds such as my own. I am slowly losing the weight and feeling like myself again and people are noticing and asking me what I have done. Even more importantly, I am passing the information on to the people I know and love. I hope they find your articles informative and take action to help heal their bodies naturally and safely, too.

  4. Mum from Norway says:

    I was just wondering when you have an autoimmune disease if you can use chia seed or Flax seed? In Your recipes for anti-inflammatory smoothie there are theese seeds but in the text over you said that we should avoid it. I think i am going to order Your e-courses to learn more aboute this. I have a daughter with ulcerøs colitt.

    • Short answer is, it depends. Some do better with flax, some do better with no seeds at all. Flax and chia do have anti inflammatory properties, so it really depends.

      • rs711 says:

        It’s useful to couch those anti-inflammatory claims within the context in which they were studied, which is to say, mostly by comparing them to conventional breakfast foods (i.e. substituting flax for conventional diet items). Would we consider flax particularly anti-inflammatory if we substituted it for a breakfast of wild-caught salmon & pastured eggs? I’d venture “no” or “not particularly”.

        However, in vitro data does show some anti-inflammatory properties & the in vivo data reflects this (but only to a very weak extent, if at all, depending on which studies you focus on).

        Flax seeds certainly aren’t a “bad choice” when talking about recommendations for the general population but it certainly isn’t amongst the best choices if we compare it to other foods.


        Legumes – we seem pretty aligned in terms of their low placement on the over all totem that considers both nutrient density p/calorie & toxic load. However, I’m seeing good arguments concerning the mechanisms by which phytates are inactivated, how dosage in studies wasn’t reflective of all real life quantities, how our microbiome can modulate/mitigate undigested particles etc… Do you have specific mechanisms you think are worth exploring further or do you think that less is best, regardless? (Not sure if that’s quite clear – hopefully you see what I’m getting at).

        I ask because it seems that it all comes back to “OK so if you really want to eat legumes/grains, then you minimize their negative impact by A, B or C…” and never do I see a good argument saying “eat these grains/legumes because it will do X, Y or Z for you that these other non-legume/non-grain foods can’t…”


  5. Holby18 says:

    A very difficult issue for me as I am vegetarian. i rely on pulses etc for nutrients.

  6. Earthkeeper Atheart says:

    Thanks for the interesting article Amy. I am concerned as others seem to be regarding vegetarianism, as many of us get our protein from organic quinoa and organic chia. In one of your responses to someones comment you mention that chia has anti-inflammatory properties as well-it would be helpful to mention this in the article. My partner has both auto-immune and ulcerative colitis and is vegetarian, and as a kinesiologist i have noted that she does badly with wheat but is fine with both quinoa and chia as amino acid/protein sources. You suggest that these should be cut out of the diet but provide no alternative for protein/mineral or omega sources. I understand that you are trying to sell ebooks but surely you should include the benefits and alternatives in your articles rather than briefly telling people to avoid these healthy food types?

  7. HCook says:

    I have been trying to research diet for Behcet’s. I am currently on many meds; dairy, beef and pork free. Trying gluten free. Now I see eggs, grains, nuts, beans, seeds and nightshade veggies are something to avoid. I am getting overwhelmed and feel like I am going to have nothing left in my diet. I also have to feed the family, who are not on board. How did you all deal with this? Any advice?

  8. sue says:

    Then can you use rice and pea protein in smoothies?

  9. […] For my patients with autoimmune diseases like Sjögren’s Syndrome, I highly recommend removing all grains and legumes from the diet as […]

  10. Sorry, people who are vegan, macrobiotic, have liver and kidney disease [ and thus cannot tolerate animal protein] need non gluten grains and legumes. The grossly high fat raw food and paleo diets so in vogue today are not for everyone.

  11. LJ says:

    You have basically listed every possible source of vegetarian protein as things to avoid- how are vegetarians supposed to get protein without causing gut damage?

    • Kim says:

      Also very interested to know this as well. And not just protein, but it also excludes nightshades, which are a huge group of vegetables and spices. For someone who is very allergic to diary and eggs, and does not eat meat, what are we supposed to do?!

  12. […] disorder known as leaky gut, which further burdens your immune system. Many other foods, including gluten-free grains and legumes, also trigger inflammation. That’s why on The Myers Way you will cut out gluten and clean up […]