The WHYs behind the Autoimmune Protocol: Nuts and Seeds

September 4, 2012 in Categories: by

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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 4Dose 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



You said “To date, there is no scientific evidence that the lectins in nuts and seeds cross an intact gut barrier or prime the immune system”

What then, is the specific evidence that the lectins in grains cross an intact gut barrier or prime the immune system?

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