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Molecular Mimicry: A Case of Mistaken Identity

by Dr. Mitchell Rasmussen, DC, CFMP, FRC-ms

The health of our gastrointestinal tract largely determines our sensitivity to various proteins and can dictate the degree of inflammation we might have from seemingly innocuous foods. If your gut is unhealthy, particularly if your gut is leaky, it is more likely that your immune system will respond negatively to potentially allergenic compounds (for example: gluten, casein, soy).

<<In fact, even in the absence of true intestinal permeability, our immune system can still pick up these problematic protein sequences through the action of Dendritic Cells!>>

Molecular Mimicry in the Context of Functional medicine

Your GI tract is what allows the right nutrients into your bloodstream and keeps out the things that aren’t supposed to be there. Similarly, if you have an imbalance of gut bacteria, you are more likely to react to sugars (re: lactose, fructose) with gas, bloating, and GI discomfort. As you heal the gut and balance the microbiome, you improve oral tolerance and may find that you tolerate foods you were previously reactive to.

The immune system is constantly asking “friend” or “foe” to any incoming proteins. When it reacts to a perceived threat, it forms antibodies which may also bind to glands and tissues that look like these proteins.

---- This is what we call molecular mimicry.

To give you an example: Gluten and Casein have similar characteristics to our own body’s tissue. When these proteins make their way into the bloodstream, the immune system attacks them and occasionally will instead attack our own tissue. It’s a major case of mistaken identity!

What is Molecular Mimicry in Thyroid Tissue

The Physiology Behind Molecular Mimicry

Molecular mimicry occurs as one consequence of a permeable GI Tract (“leaky gut”). When the tight junctions between the intestinal lining cells break down, this not only leads to less absorption of the nutrients you need BUT also can allow endotoxins (lipopolysaccharide) and other proteins into the bloodstream.

These invaders cause your immune system to go on alert. However, the immune system can never adequately resolve these issues because they are being supplied by our lifestyle (and poor dietary choices). The immune system works to neutralize these endotoxins by creating antibodies and inflammation. Your immune system begins to attack its own tissues, thus further propagating a far-away dysfunction at the cellular, tissue, glandular, and whole-body levels.

(!!) When immune antibodies are formed to gluten or casein, they can also be formed against brain cells and thyroid cells. Thus, the cycle is perpetuated: Eat gluten, thyroid condition gets worse — Have thyroid disease, gluten makes it worse.


What we find clinically is this:

If we find thyroid antibodies, we will absolutely recommend a gluten-free and casein-free diet at least as a trial intervention.

While we are not going to preach that EVERY patient needs to avoid gluten and dairy, certain conditions absolutely require strict avoidance for symptom management. We use functional lab testing to help direct nutrition guidance; and antibody testing is included even in our baseline bloodwork. However, in the absence of testing, an elimination diet is the first step in determining how certain foods or food groups may be affecting you.


Elimination Diet PDF Guide by Functional medicine doctor and functional nutritionist

Mitchell Rasmussen Functional Medicine Doctor Denver Colorado

Dr. Mitchell Rasmussen, DC, CFMP serves as Director of Functional Medicine at The Facility in Denver, CO. He sees patients in-person and via Telehealth to get to the root cause of dysfunction and restore a state of well-being using nutritional intervention, supplementation, and lifestyle change.


Functional medicine Denver co

Want to work with a functional medicine doctor to run labs and assess nutrient status? Struggling with hormone imbalance, IBS, weight gain, mood changes? Let's look at BIOCHEMISTRY. Read more about Functional Medicine at The Facility here.

Not sure where to start?

CLICK HERE to schedule a FREE 15-Minute Consult with Kate to determine your best course of action!

Or reach out by email


Understanding Molecular Mimicry in the context of Functional Medicine - The Facility Denver


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Dr. Mitchell Rasmussen - Doctor of Chiro
Kate Daugherty - Nutritionist - Function
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