The WHYs behind the Autoimmune Protocol: Eggs

June 23, 2012 in Categories: , by

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Eggs are one of the most allergenic foods with approximately 2-3% of the population affected.  However, people are still surprised when I advertise an egg-free recipe or mention that I can’t eat eggs.  It’s not because I’m allergic but because I have an autoimmune disease and eggs are excluded on the Autoimmune Protocol.  Given that eggs are such an important staple for the paleo enthusiast (as a breakfast food, as a cheap protein, and as an ingredient in the vast majority of paleo baking recipes), I get asked “Why Eggs?” frequently. 

One of the main functions of the white of the egg is to protect the yolk against microbial attack while the embryo grows.   It achieves this worthy goal by using proteolytic enzymes (or proteases), enzymes that can cleave proteins into shorter chains of amino acids (typically rendering those proteins inactive/useless in the process).  There are many different types of proteolytic enzymes, each highly specialized to cleave a specific type of protein and/or in a specific place.  In particular, the proteolytic enzymes in egg whites are very good at cleaving proteins in the cell membranes of certain bacteria (specifically gram-negative bacteria, which I’ll come back to in a couple of paragraphs).  The specific protease in egg whites that those of us with autoimmune disease (or severe allergies or severely leaky guts) need to be concerned with is called lysozyme. 

I used to use lysozyme in the biology lab to break apart the membranes of bacteria (typically bacteria that I had engineered to grow specific DNA strands for me).  Lysozyme is specific for bacterial membranes, works very quickly, is very resistant to heat, is stable in very acidic environments (so it’s still active even after cooking eggs thoroughly and digestion!), and is really a pretty ingenious little enzyme (that’s me geeking out).  Humans also produce lysozyme as part of our normal defense mechanisms against bacterial infections.  It is present in our saliva, tears and mucus (including the mucus layers in the intestines).  So, if we already make our own lysozyme, why is it a problem in egg whites?

Lysozyme has the ability to form strong complexes with other proteins.  So, lysozyme from egg white typically passes through our digestive system in large complexes with other egg white proteins.  Many of the proteins present in egg whites are protease inhibitors (see this post for more information on how protease inhibitors can contribute to a leaky gut).  This means that the lysozyme/egg white protein complexes are resistant to digestion by our digestive enzymes (which are themselves proteases).  You might be wondering if lysozyme is still active if it is a protease and it is now bound to egg white protease inhibitors.  The answer is yes, it is still active.  The egg white protease inhibitors that are most likely to be bound to lysozyme are ovomucin and ovastatin, which are a trypsin inhibitors (trypsin is one of our main digestive enzymes), cystatin, which is a cysteine protease inhibitor, and ovoinhibitor, which is a serine protease inhibitor.  None of these inhibitors inhibit the activity of lysozyme.  And very importantly, as the lysozyme complex travels (largely intact) through the environment of our gut, lysozyme can also bind bacterial proteins from the bacteria normally present in our digestive tract (like the gram-negative E. coli!). 

Lysozyme has an unusual chemical property (it maintains a positive charge) that allows it to cross through the enterocytes by electrostatic attraction to negatively charged proteins imbedded in the enterocyte cell surface (proteoglycans).  Research confirms that consumed lysozyme gets into the circulation even in healthy individuals (even in conjunction with food intake, although the amount that enters the circulation is lower). 1,2,3Absorption of pure egg white lysozyme by itself into circulation is likely not problematic because lysozyme is an enzyme that the body naturally produces (unless it is absorbed in very high concentrations and then it can cause kidney damage).  The problem is the other proteins that piggyback on lysozyme across the gut enterocyte barrier.  It is this “leak” of other egg white proteins that is the reason why egg allergy is so common.  Any other proteins present in the digestive tract can potentially bind in the lysozyme complex and get helped across the gut and into the blood stream (or lymph).  And because lysozyme binds bacterial wall proteins, these are likely to “leak” across the gut enterocyte layer as well.  These foreign proteins are believed to contribute to a molecular mimicry response where the body, in its attempt to form antibodies against these foreign invaders, accidentally creates an antibody that also recognizes a normal protein in the human body. 

It’s also important to point out that the ability of lysozyme to cross the gut barrier (carrying potentially immunogenic proteins along with it) is a fairly small effect.  In normal, healthy individuals, lysozyme is not likely to cause significant damage to the healthy lining of the gut or cause a substantial immune response (although the effect of lysozyme is why Prof. Loren Cordain recommends limiting eggs to 6 per week).  In healthy individuals, pastured or omega-3 eggs can be an excellent, inexpensive source of protein, omega-3 fatty acids, lutein, zeaxanthin, choline, selenium, phosphorus, vitamin A, vitamin D and the B vitamins.  However, in the case of autoimmune disease, individuals are more sensitive and tend to have exaggerated immune and inflammatory responses to foreign proteins in the circulation.  These individuals are also more likely to form auto-antibodies in response to bacterial proteins that may enter into the circulation with lysozyme. 

You might notice here that this discussion was entirely related to egg white proteins.  Egg yolks are not likely to cause these issues.  However, if you are following the Autoimmune Protocol, I urge caution since egg yolks are a very common food sensitivity in those with leaky guts (note that this is different than being allergic to them).  I still recommend avoiding both egg white and yolk when you first adopt the Autoimmune Protocol.  But, of all of the foods that are restricted in this protocol, I think egg yolks are the most likely to be tolerated and many people can add them back in. 

1 Kondor-Koch C, et al.  Exocytotic pathways exist to both the apical and the basolateral cell surface of the polarized epithelial cell MDCK. Cell, 1985. 43(1): 297-306,

2 Hashida S, et al. Concentration of egg white lysozyme in the serum of healthy subjects after oral administration. Clin Exp Pharmacol Physiol. 2002.  29(1-2):79-83.

3 Nishikawa M, et. al. Electrical charge on protein regulates its absorption from the rat small intestine. Am J Physiol Gastrointest Liver Physiol. 2002.  282(4):G711-9.


Thank you for your in-depth understanding of eggs and their digestion. I am glad you provided a response that is calculative in nature. Good memory skills!

If I am taking and enzyme supplement, and that supplement contains lysozymes is that problematic? Or are you saying because it is in its isolated form it is fine?

Thank you so much for the egg white explanation. I a, healing from Lyme and so have chosen an autoimmune diet. This visual actually gives me more motivation to stay off the eggs…:( I love them though.

while trying to read your interesting information, you keep interrupting me with stupid requests for my e-mail address, which just causes me to give you a fake address just to get rid of the stupid message. Why do you do this?

Click the X button in the upper right of the window to close it without entering your e-mail address if you do not want to subscribe to Sarah’s newsletter. Once you close the window, it never appears again. – Christina, Sarah’s assistant

What about substituting duck eggs for chicken eggs? I tested positive for an egg sensitivity, but was told I could still eat duck eggs.

Hi. Thank you so much about the info on egg yolks. I really want to add them back in, but am not sure how many weeks I have to wait? I am not sure how much chicken liver I can eat in a week to make up for missing the yolks (I have a very hard time with beef liver).
Any advice would be stellar! Thank you.

So I just tried olive oil based hollandaise last night (rinsing the yolks very very well before using) and had a couple rinsed and fried egg yolks this morning. They are a no-go. :( I developed a sore in my throat where my tonsils used to be, like I always do when stuff doesn’t apgree with me, along with some light palm and foot itching. Not sure if I can introduce them after the trial period again? Is anyone successful reintroducing them even after experiencing symptoms?

Could consumption of at least two eggs per day be implicated in an outbreak of lichen planus, especially as it is an autoimmune disorder?

Ok, so the gram-negative E. coli normally present in our guts, is that the ‘good’ E. coli, that helps us poop? So eggs bind proteins that the E. coli needs? Sorry but I’m still trying to sort this out in my head…. if I’m understanding this right the lack of the good E. coli would contribute to constipation, correct? I have struggled with this my whole life. I eat alot of eggs. I’ve been known to go through a dozen in less than a week. I need more help understanding this E. coli angle.

Are the antibodies of concern mentioned here for autoimmune patients the same as those tested through IGg food sensitivity test?

could you please provide some references for the stability of lysozyme at regular baking temperatures, I’ve tried looking for them and from what I found it seems the enzyme would be pretty much done at those temperatures.


I have been having multiple health issues the last four years that doctors have no real answers to or blame it on my auto immune disease, rheumatoid arthritis which I was diagnosed with year ago at the age of 10. However I went to a hololistic doctor who told me to try the paleo diet. I have been reading for auto immune you should not eat eggs or nuts or seeds, however I have been tested for these and everything came out fine, do I still need to avoid these items if i am not allergic to them?

I am attempting to do the AIP while breastfeeding a 7 week old as I have Hashi’s and Celiac (and eczema and anxiety,) and I am worried my leaky gut is minimizing the nutrition I am absorbing, giving me less to give to him in my breastmilk. Another major reason for me wanting to do AIP now is because baby has shown negative reaction to something I am/have eating/eaten (thinking dairy but jury is still out while my body and his flush it out) with mucous-y poops, mild eczema, seeming “constipated”/straining a lot and gassiness/fussiness, of which the latter two seemed to improve but not disappear immediately with removal of most dairy. BUT I have been told that egg yolks are the best source of choline and that choline is vital for babies in utero up to 3 months of age, and since I couldn’t stomach eggs during pregnancy, I have wanted to include more egg yolks in my diet at least until he reaches 3 months. I have not added them yet in the frequency I would like, though, as I know they are a no no.

I am thinking hard boiling would be the best and easiest way for this new mama to enjoy yolks while separating the most white from them. Do you think that this is a good call for baby to get choline OR are hardboiled yolks going to be just as likely a culprit in baby’s potential food allergies? I hate seeing him suffering from something I am doing unknowingly. :(

Much thanks from Alaska!

I was diagnosed with Hashimoto’s and at the time also tested positive for egg antibodies. My Hashimoto’s is in remission (no more antibodies). Should I still avoid eggs?I’ve never noticed any symptoms when eating them.

Taking delight in figuring things out and the process of life is not “geeking out.” I wish you wouldn’t insult yourself just because you enjoy something. It’s a sign of the sickness of our society that things you like should be somehow “shameful.”

I did a pen allergy/intolerance test and egg whites came out in the top three of things for me. I noticed I didn’t quite feel right after eggs (before the test) but I was still upset to see it come up on the list. I do miss eggs so, so much but I’m learning to find alternatives. It makes Paleo breakfasts s bit harder!!! Im not sure I can ever go back to eggs (I tried recently following months of not eating them) and it didn’t work :(

Hi! Dr. Ballantyne, I seem to tolerate Duck eggs better than chicken. In my son’s case he completely reacts to Chicken eggs but not at all – that we can assess – to Duck eggs. I understand it’s because Ducks eggs are alkaline. Do Ducks eggs have the impact you describe above?

The article states that egg yolks are usually easily reintroduced. I’m wondering if there’s a recommended time frame to try and reintroduce? I’ve only just decided to start researching and preparing for the AIP as someone who’s hypothyroid, but I’ve been reluctant because I am a pescetarian. I figure I can eat a lot of fish while I’m on the AIP, but it would be great to have eggs as an option sooner rather than later. Would you recommend reintroducing the egg yolks after a week or two or would that be too soon? I can certainly wait for the whites until later.

When I originally left a comment I seem to have clicked the -Notify me
when new comments are added- checkbox and now each time a comment is added I
receive four emails with the exact same comment. Is there a way you can remove me from that service?


We have chickens and eat their eggs. My husband use to have very bad gas from eggs but since we are raising eggs he hasn’t had any problems. That being said, is it what chickens are being fed that is causing the problems with gut health and allergies?

That is certainly a possibility. Some people are so sensitive to things like soy or grains that are common in chicken feed that they will react to the eggs produced from the chickens that are fed these things. -Kiersten

Hi. If I tested negative to a yolk and white sensitivity, should I still refrain from eating them? Thank you.

Do you think people have problems with eggs becuse of use in the creation of vaccines. I mean, vaccines create an immune response to the antigen, so why would they not create an immune response to any of the other ingredients?

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