The WHYs behind the Autoimmune Protocol: Nuts and Seeds
September 4, 2012 in The WHYs of the AIP
When it comes to understanding the whys behind the extra restrictions of the autoimmune protocol, it is usually easy to see the link between certain foods and increased intestinal permeability and/or interaction with the immune system. In the case of nuts and seeds, however, it is actually much harder to make a very strong case for their removal from the diet for those with autoimmune conditions.
There are plenty of books and websites that list all nuts and seeds as foods to avoid on the paleo Autoimmune Protocol (for example, The Paleo Solution, It Starts With Food, and Practical Paleo). The rationale ranges from none to a simple statement that nuts contain lectins and phytic acid. However, as I have delved deeper into this subject, the science behind this argument is lacking.
It’s not about lectins. As I have mentioned before, lectins are a class of sugar-binding proteins with a variety of functions in both plants and animals. Almost every food contains lectins and this fact by itself is not sufficient to avoid eating something (otherwise we wouldn’t eat anything!). The lectins that we avoid eating on a paleo diet are lectins such as gluten (and related lectins in other grains and legumes) that are known to survive cooking, be poorly digested, interact with the cells that line the gut, increase intestinal permeability and/or cross the intestinal barrier largely intact where they can stimulate the immune system. To date, there is no scientific evidence that the lectins in nuts and seeds cross an intact gut barrier or prime the immune system.
It’s not about phytic acid (well, not much, anyway). Nuts are relatively high in phytate, which is the salt of phytic acid, i.e., it is phytic acid bound to a mineral. These minerals are not available for absorption, which is why consuming large amount of foods high in phytic acid and/or phytate is not a good idea (it leads to mineral deficiency). And it certainly means that the minerals found in nuts are not really a good rationale for eating nuts, if we can’t absorb them very well (although I should mention that your gut microflora help release the minerals for you to absorb). Consumption of excessive phytic acid/phytate may irritate the lining of the gut and contribute to a leaky gut by reducing the activity of a variety of digestive enzymes, including trypsin 1, pepsin 2, amylase and glucosidase 3. However, phytate may also be an important antioxidant and help reduce cardiovascular risk factors and risk of developing cancer when consumed in moderate quantities 4. Dose is important here. But, this is an argument to limit nut consumption, not cut nuts out of our diets completely.
It isn’t about the omega-6 content of nuts. Nuts tend to have much more omega-6 polyunsaturated fats than omega-3 polyunsaturated fats. So, when one of the main goals of a paleo diet is to normalize the ratio of omega-3 to omega-6 fatty acid intake, eating large quantities of nuts is not helpful. With the importance of resolving inflammation for those with autoimmune condition, increasing the amount of omega-3 fatty acids (and simultaneously decreasing omega-6 fatty acids) in the diet is critical. Even walnuts, which have the highest omega-3 content of all nuts have a 1:3 ratio of omega-3 to omega-6, and these omega-3 fats are the short chain ALA fats which are not as readily used by the body as the longer chain DHA and EPA that are found in seafood and grass-fed meat. Macadamias are the exception with the vast majority of their fat being monounsaturated. However, in a diet rich in fish and grass-fed meat, small quantities of nuts that are conscientiously consumed should not be a problem.
So, why are nuts so uniformly restricted on the paleo autoimmune protocol? Actually, they aren’t. Two prominent examples are the opinions of Prof. Loren Cordain, author of The Paleo Diet and The Paleo Answer, and Dr. Terry Wahl’s, author of Food As Medicine and Minding My Mitochondria and well-known for her TedX-Iowa Talk. Prof. Loren Cordain hesitantly recommends their removal for those with autoimmune disease with the following caveat: “In addition to peanuts, which are not a nut at all, but a legume, tree nuts (almonds, walnuts, pecans, brazil nuts etc) are one of the most common allergenic foods. To date, tree nuts have been poorly studied for antinutrient content, and it is unclear if they increase intestinal permeability of adversely affect the immune system. This would be one of the last foods I suggest restricting [for those with autoimmune disease].” 5. Dr. Terry Wahl’s lumps nuts in with grass-fed dairy and thoroughly-cooked sprouted legumes as foods she consumes “very little” of but doesn’t restrict altogether 6.
It boils down to two simple facts. Tree nuts are one of the top allergens and most common food sensitivities. People with autoimmune disease are very likely to have a leaky gut, which increases their susceptibility to developing food allergies and food sensitivities (the difference is in the type of antibody formed). This means that people with autoimmune disease are more likely to have a sensitivity or allergy to nuts (and seeds) than other people. And cutting nuts out of the diet using an elimination diet approach such as the autoimmune protocol is a good way to isolate whether or not nuts are a problem for you. If you continue to eat something that you have an allergy or sensitivity to, it is very difficult for your gut to heal and for your immune system to deactivate.
Additionally, the fiber in nuts and seeds can be difficult to digest, particularly almonds, pistachios and hazelnuts (read my FODMAP post), which is an additional way that some people can be sensitive to them.
I personally have found that avoiding almonds has been very important for me although I seem to be able to handle small amounts (like 1-2 ounces) of other nuts (typically macadamias, walnuts and pecans). Larger amounts of nuts do seem to be a problem for me and I attribute this to the omega-6 contribution that they make to my diet. I still think it’s important to remove nuts and seeds from your diet, at least for a month, when you first start the autoimmune protocol. However, unlike tomatoes or egg whites, which have a much higher ability to be problematic, reintroduction of individual nuts and seeds should only worsen your symptoms if you have a sensitivity.
1 Singh M and Krikorian AD “Inhibition of trypsin activity in vitro by phytate” J. Agric. Food Chem., 1982, 30 (4), pp 799–800
2 Vaintraub IA and Bulmaga VP.“Effect of phytate on the in vitro activity of digestive proteinases” J. Agric. Food Chem., 1991, 39 (5), pp 859–861
3 Kunyanga CN et al “Antioxidant and type 2 diabetes related functional properties of phytic acid extract from Kenyan local food ingredients: effects of traditional processing methods.” Ecol Food Nutr. 2011 Sep-Oct;50(5):452-71.
4 Food Phytates; N.R. Reddy and S.K. Sathe, editors. 2002
5 http://thepaleodiet.com/hidradenitis-suppurativa/
6 http://www.thepreparationstation.com/2011/terry-wahls-md-cured-her-ms-with-a-paleodieta-paleodiet/





































Sarah, I will be starting the auto immune protocol in a few days and I’m both hesitant and excited. My family and I have been on the Paleo diet since the end of March and we’ve been doing really well. I was diagnosed with vitilgo 5 years ago. It’s only in the last year that I’ve finally made the connection between my diet and my health. This will be my next big step and I’m looking forward to some positive results. All the information you share is every encouraging. Thank you!
[...] Nuts [...]
Hi Sarah! What about cashews… where do they fall on the list?? I have been on the AIP for 2 months with no nuts at all (and seeing this post makes me think it’s time to try to add something back!)
thanks!
Cashews can have issues based on being a nut/drupe and also because they come from the same family as poison ivy. Some people will be sensitive to them and not other nuts, and vice versa. I would try them, up to you what order (remember to just try one type of nut at a time, giving 3-4 days in between).
thank you!! I see them in GAPS recipes all the time and was curious about them!
It was really timely for me to read this. I have been following the Paleo AI protocol for only a week…but I haven’t dropped nuts and seeds yet as it all seemed a bit overwhelming. I have Grave’s Disease and Celiacs. I have been egg and dairy intolerant for about 18 months. My doctor is certain I have leaky gut. I have found taking out all grains and nightshade vegetables has made a HUGE difference in just a week. I actually don’t have brain fog anymore and I am sleeping again. I will now take out the nuts/seeds as well..
This is encouraging. I got rather depressed after your nightshade post as it made me realize I may never get my beloved peppers back. But after reading this, I am at least hopeful that I can try adding the seed spices back in at some point – hello cumin and coriander. I also have Graves and am struggling a bit to get fully on board with the protocol. I come here pretty much daily for some inspiration and motivation as understanding the WHYs really helps me stay on track.
Most nuts are high in salicylates and oxalates, which can be very hard on the gut. Almonds are the worst perpetrator in this regard.
[...] Seeds (except sesame seeds) [...]
Thank you. What does this mean? “However, unlike tomatoes or egg whites, which have a much higher ability to be problematic, reintroduction of individual nuts and seeds should only worsen your symptoms if you have a sensitivity.”
It means that tomatoes and eggs can cause problems through mechanisms different than the immune reactions that happen in the case of food sensitivities. Specifically, the lysozyme in egg white can act as a transporter for foreign proteins across the gut and the saponin alpha-tomatine in tomatoes can ramp up an immune reaction through its adjuvant activity.
What about homemade nut milk?
Some people tolerate it better than nuts because soaking removes the some of the anti nutrients and removing the pulp gets rid of most of the fiber. But, if you are sensitive, you will still be sensitive to nut milk. I definitely recommend leaving it out in the beginning.
Does this include fruit seeds — e.g. pomegranate seeds?
Seeds in fruit are meant to be eaten (and then planted in very fertile soil on the other end of the digestive tracts) compared to seeds that are designed to be spread by wind, etc. I consider foods with edible seeds (pomegranate, berries, zucchini, cucumber, etc.) to be a gray area. Some people tolerate them and some don’t (similar to berry spices).
This article is so informative ! Thanks so much. I had to start an anti-TNF called Remicade one month ago. This treatment is the only one which relieves me, after having tried to heal naturally then with different drugs.
The bad news is I can not do any food allergy testing while on this drug. Before I started Remicade, I became allergic to almost everything ( Crohns, severe pain in stomach)in a 2 month time . It was impossible to identify the culprits. I have a deep feeling that sprouted bread – even small amounts, but repeated over one month – has been the initial trigger for my flare, then eggs.
I had no grains and no eggs for the last 3 months and might l avoid them for good. I have re-introduced almond butter and macadamias on a daily basis, without any pain. Do you think it is possible that my body is not allergic anymore to nuts as my gut is healing ? Or is it just hidden by the fact I am having a medication which hides a possible allergy ?
I think it’s more likely being masked by the medications. I typically recommend that people follow the strict autoimmune protocol until their symptoms are on remission and their need for medications ceases. That being said, it is still completely possible that you may be able to reintroduce them successfully.
Does this include coconut?
Coconut milk and oil are fine. Whole coconut products like flour, butter and shredded should be used in moderation.
How does food allergy/sensitivity testing play into this? I have an Hashimotos and recently got my food allergy/sensitivity test done. Many of the ones I already suspected showed up (gluten/wheat/barley, dairy, tomatoes, coffee), and I have already cut those out anyway. The only nuts that showed sensitivity were peanuts and walnuts. I did not show any significant sensitivities to almonds or cashews. I am starting a strict elimination period based on all the foods that showed sensitivities, but should I also cut out all nuts and seeds during this period as well? I guess what I am asking is, can I use food sensitivity testing as a basis for which nuts and seeds I can eat, or is it still a good idea to go through the elimination and reintroduction process to make sure?
You can be sensitive to these foods in ways that don’t show up on tests. It would be safer to eliminate at first.
If the leaky gut is the reason for nuts causing food allergies than reintroducing them after leaky gut is healed should be fine.
On the omega 6 content the “small amounts” needs to be emphasized though. To balance omega 6 from 100 grams of walnuts one needs to eat 1 kg of salmon.
What about chia seeds? I have Hashimoto’s. Have gone gluten-free and am educating myself about/ working toward a transition to Paleo. Introduced chia seeds a few months ago, and the only change I’ve noticed is that I’m not losing nearly as much hair in the shower every day.
Chia seeds are a pseudograin and not included on the AIP.
I love almonds and ate a ton of them without issue before trying the AIP. Other nuts (pecans, walnuts, macadamia) I had to limit because they were migraine triggers. (Just as background, I have been gluten free for about 3 years–celiac testing was negative but I had been gf for a year before they tested me, dairy free for 20 because of sensitivity, and have a severe shellfish allergy, My husband went paleo over a year ago so I’ve been mostly paleo since then (still would do gf flours occasionally) However, after almonds for 45 days of autoimmune I decided to try a reintroduction and everytime I have almonds or almond flour I get stomach pain and bloating. Wth? I ate almond butter on everything without noticing a reaction, why would avoiding it and then reintroducing it allow the reaction to show? I’ve successfully reintroduced eggs (but I limit them) and nightshade spices without reactivity. I would appreciate hearing your thoughts. Thanks!
The whole point of an elimination diet is that it allows you to see those reactions more clearly. There’s two reasons: your body has natural defense mechanisms to protect itself from foods that harm it (like increasing the thickness of the mucus layer in the gut). When you cut out a food that you are sensitive to, you stop protecting yourself against it, so when you have it again, the reaction is bigger. The other reason is that when you eat something frequently, you don’t necessarily really notice that you feel a little crumby when you eat it. Stopping for a while, you gradually feel better and better, then when you eat that food and feel crummy like you used to, it feels more dramatic because it’s been a while since you felt that way and you feel so good now.
I knew you would be able to explain it. I so appreciate you! Your blog is the one thats made paleo and AIP do-able for me because you explain it in a way that makes sense. Thanks!
What a wonderful post, OMG I have just learnt so much more about the AIP. I thought I knew everything about paleo….Thank you so much! ?:-)
Quick questions – how about chestnuts and squashes/pumpkins? Winter types. I prefer to use them instead of fruit for denser carbs, are they ok?
Chestnuts seem to be ok with me – Crohns disease – but regular nuts and seeds are not as you suggested. I can get whole or grated chestnuts here in Hungary and they are a good carb source I assumed. Should I ditch them for now? Thank you!
I normally wouldn’t recommend chestnuts, but if you feel like they are working for you, i think you should keep eatign them. Squashes and pumpkin are awesome.
Thanks so so much again for all your help and great posts!:-)
I was leading a candida diet for alopecia and I guess it all leads back to the same thing with autoimmune diseases; heal our guts and eat non-inflammatory foods. I am going to do the even stricter AIP now. Wondering if hemp seeds are a no?
Hemp seeds are a no.