5 Shocking Truths About Leaky Gut and Food Allergies (The Missing Thyroid Gut Connections)

By |2017-04-25T00:15:47-07:00January 26th, 2016|Hypothyroidism|20 Comments

This is Part 2 of a 3-part series on hypothyroidism and gut health:

Forget about food allergies…

I know… You might be thinking that healing your gut and addressing your food allergies is the answer to your hypothyroidism or Hashimoto’s.

But odds are you’re only making your thyroid condition and gut health worse.

And I say this from experience.

Long ago, we used to run food allergy or food sensitivity labs on almost all of our clients.

We followed the commonly prescribed approach today of food avoidance combined with various anti-inflammatory and gut health supplements.

The only problem was that… it didn’t work.

While we oftentimes saw short term improvements in our clients… it was the long term problems that had us worried.

In the long term the majority of our clients regressed and eventually their symptoms returned, oftentimes worse than before.

This was one of the many reasons why we began to re-think our approach to gut health entirely.

And it wasn’t until we discovered the missing thyroid gut connections (which I’m about to share with you) that we ever saw real and consistent results.

Most people with leaky gut have become so afraid of foods that they don’t even know what to eat anymore.

Yet in most cases, the real problems have little to do with the foods themselves.

At least not the foods you might be sensitive to.

And how are you supposed to repair your leaky gut when many of the health foods and supplements you’re using to heal it are also known to cause it?

You see… the approach that most people take is completely backwards.

And you end up worse off than when you started.

If you want real results, then it all starts with understanding and fixing these missing thyroid gut connections.

When we do that, our clients not only experience long term improvement in gut health, they oftentimes experience a complete resolution of their food sensitivities.

So, let’s get into it, but first…

What Is Leaky Gut?

If you’re not familiar with leaky gut, then a picture can be worth a thousand words.


Leaky gut (intestinal permeability) is a condition where the space (gaps) between your cells that line your intestines become wider, allowing for various particles within your digestive tract to “leak” directly into your bloodstream.

These cell gaps are designed to be small, only allowing nutrients to be absorbed.

However, when these cell gaps become enlarged, they allow larger particles to enter your blood stream resulting in a heightened immune response.

Leaky gut is known to play a direct role in many inflammatory related digestive conditions include…

  • Celiac Disease
  • Irritable Bowel Syndrome (IBS)
  • Inflammatory Bowel Disease (IBD)
  • Crohn’s Disease
  • And others

However, it’s also involved with a number of other digestive related conditions including colon cancer.

Increased tight junctional permeability is associated with the development of colon cancer


“These results showed that increased TJ permeability [leaky gut] of the colon epithelium and consequently a decrease in epithelial barrier function precede the development of colon tumors.”

There’s no denying that leaky gut is a serious condition with serious health consequences.

But what happens when many of the health foods and supplements you’re using to improve your gut health are actually making it worse?

1. The Leaky Gut, PUFA, and Fish Oil Connection

Let me ask you two very important questions…

  1. Are you cooking with “heart healthy” fats and oils?
  2. Are you supplementing fish oil or omega-3s?

If you answered “YES” to either of those questions then I hate to be the bearer of bad news but…

You’re partly to blame for causing your own leaky gut.

For decades now, doctors, nutritionists, dieticians, etc. have been pushing polyunsaturated fats (PUFAs) as “heart healthy” while research continues to show just how dangerous they really are.

Not only do they…

They are also well known to cause leaky gut.

The type of dietary fat modulates intestinal tight junction integrity, gut permeability, and hepatic toll-like receptor expression in a mouse model of alcoholic liver disease.


“CONCLUSIONS: We demonstrate that USF (corn oil/linoleic acid) by itself results in dysregulation of intestinal TJ integrity leading to increased gut permeability [leaky gut], and alcohol further exacerbates these alterations.”

(Source: http://www.functionalps.com/blog/2012/07/04/fish-oils-increases-intestinal-permeability/)

(Note: Not sure what PUFAs are, or what fats I’m referring to? Check out this article on the “5 Worst Cooking Oils for Your Thyroid”.)

And what about that fish oil or omega-3 supplement you might be using?

Many are using these supplements for the specific purpose of reducing inflammation, especially in the intestines.

Well, you might be surprised to learn that fish oil and omega-3 fatty acids (both of which are PUFA) also contribute to leaky gut.

Ingestion of (n-3) fatty acids augments basal and platelet activating factor-induced permeability to dextran in the rat mesenteric vascular bed.


“Our data suggest that augmented intestinal barrier permeability [leaky gut] to fluid and macromolecules is a possible side effect of (n-3) FA-rich diet supplementation.”

(Source: http://www.functionalps.com/blog/2012/07/04/fish-oils-increases-intestinal-permeability/)

Interestingly enough, saturated fats which are commonly and wrongfully demonized have no negative effects with respect to leaky gut.

(Note: In the 3 Food Triple-Thyroid-Boosting Daily Protocol, I show you one of the most important fats we use to help boost thyroid function.)


You can download this daily protocol here.

2. The Leaky Gut Endotoxin Connection

Have you ever heard of the term “endotoxin”?

It happens to be one of the biggest causes of leaky gut, yet few people have heard of it or even know what it is.

It has a great deal to do with your thyroid health, or lack thereof.

Research has shown that hypothyroidism itself commonly leads to a condition called small intestinal bacterial overgrowth (SIBO).

Association between hypothyroidism and small intestinal bacterial overgrowth.


“CONCLUSIONS: The history of overt hypothyroidism is associated with bacterial overgrowth development. Excess bacteria could influence clinical gastrointestinal manifestations. Bacterial overgrowth decontamination is associated with improved gastrointestinal symptoms.”

And it is these unwanted and harmful bacteria that have found a home within your intestines that produce this toxic substance known as endotoxin.

As bacteria and endotoxin accumulate in your intestines it results in a number of harmful and wanted effects, including leaky gut.

A single dose of endotoxin increases intestinal permeability in healthy humans.


“These data suggest that a brief exposure to circulating endotoxin increases the permeability of the normal gut [leaky gut]. These observations are consistent with the hypothesis that during critical illness, prolonged or repeated exposure to systemic endotoxins or associated cytokines may significantly compromise the integrity of the gastrointestinal mucosal barrier.”

But what might be even more concerning is that endotoxin also increases estrogen and further promotes estrogen dominance, which further suppresses your thyroid and liver.

(Note: I cover how estrogen suppresses your thyroid and liver in detail in this article on “How to Heal Your Thyroid By Healing Your Liver”.)

3. The Leaky Gut Thyroid Hormone Connection

Do you have adequate thyroid hormone to repair your leaky gut?

I often mention that thyroid hormone (T3) is necessary for the health and function of every single cell of your body.

The cells that line your digestive tract are no different.

When the cells that line your digestive tract don’t get adequate thyroid hormone and/or can’t produce adequate energy, they lose their rigid cellular structure.

This lack of cellular energy production is one of the primary mechanisms that lead to leakiness or permeability of all cells.

And when this occurs to the cells of your intestinal lining, it results in leaky gut.

4. The Leaky Gut Intestinal Inflammation Connection

Are foods really the cause of all your intestinal inflammation?

Sure, there are foods that are known to cause intestinal inflammation.

Take gluten for example.

We always recommend avoiding gluten.

But the issues of gluten intolerance and celiac disease are also linked to estrogen dominance.

And estrogen dominance is a direct result of your hypothyroidism.

In fact, endocrine researcher Dr. Raymond Peat has mentioned…

“Celiac disease is more prevalent among females, and it involves the immunological cross-reaction to an antigen in the estrogen-regulated transglutaminase enzyme and the gluten protein.”

In other words, estrogen dominance makes you susceptible to gluten intolerance and intestinal inflammation.

And if you’ve been avoiding gluten for some time, then you likely already know that avoiding gluten alone is not the answer.

There are many other thyroid related factors that directly result in inflammation, both directly within your digestive tract and systemic.

For example, we previously covered how hypothyroidism results in bacterial overgrowth in the intestines.

But what I didn’t mention was that these bacteria are also responsible for inflammation and direct damage to your intestinal lining.

Effects of an enteric anaerobic bacterial culture supernatant and deoxycholate on intestinal calcium absorption and disaccharidase activity.


“Electron microscopic evidence showed degeneration of microvilli, disruption of mitochondrial structure, and swelling of the endoplasmic reticulum after exposure of the intestinal loops to the supernatant or deoxycholate.”

5. The Sooner You Break the Leaky Gut – Thyroid – Stress Cycle Connection the Better…

The one thing we haven’t covered yet is that chronic stress is also known to cause or contribute to leaky gut.

And while all of the missing thyroid-gut connections we’ve covered so far are responsible for your leaky gut…

…it’s the combination of these gut-thyroid connections and chronic stress that has you trapped in a cycle that is difficult to escape.

We call it the Leaky Gut – Thyroid – Stress Cycle and here’s how it works

  1. Hypothyroidism sufferers naturally compensate for the hypothyroidism by over-activating their body’s stress response…
  2. This over-production of stress hormones increases the absorption of bacterial endotoxin inside your intestines…
  3. This increased absorption of endotoxin increases estrogen…
  4. This increased estrogen further suppresses your thyroid function and further activates your stress response…
  5. And so the cycle continues…

The key to breaking this dangerous cycle is to address all of these connections together.

Improve energy production of the cells that line your intestines…

Eliminate the bacterial overgrowth in your intestines and the bacterial endotoxin that goes with it…

Detoxify and lower your estrogen levels…

And suppress your stress response while regulating your thyroid.

Sure, you can keep doing what you’re doing…

…avoiding more and more foods while your gut health worsens and you become increasingly afraid of every bite you take.

You can continue relying on foods and supplements known to make your gut health worse.

Or, you can address these missing thyroid gut connections, these real underlying problems that are causing your leaky gut.

Ultimately, the choice is yours… which path will you take?

About the Author:

Tom Brimeyer is the founder of Forefront Health and the creator of the popular Hypothyroidism Revolution program series. Specializing in thyroid and metabolism disorders, Tom's work has impacted over 50,000 people spanning more than 60 countries. Tom is also a highly sought after practitioner who runs a successful health consulting practice where he continues to help clients across the globe to take back control of their lives from their devastating health conditions.


  1. Laura January 26, 2016 at 8:54 am - Reply

    Wow. I told my doctor Fish Oil made me feel ill and stopped taking it, despite his protests. However, I’ve been using Flax Seed and Chia seed, which also contain Omega 3, because they don’t have the same affect of making me feel ill. I’m gathering this may be the wrong thing to do as well.

  2. Tina January 26, 2016 at 9:10 am - Reply

    Great information, thank you. So what’s the solution here?

  3. Vicki January 26, 2016 at 11:48 am - Reply

    Thanks great information but what can you take if you cannot tolerate coconut oil either? Is that no oils – willing to do what it takes here 🙂

    • Tom Brimeyer January 26, 2016 at 11:53 am - Reply

      Hi Vicki, it would depend on why you don’t tolerate it? Could be using the wrong type, bile issues, etc.

  4. Kristi January 26, 2016 at 9:35 pm - Reply

    So if we are to avoid pufas or unsaturated fats we should use saturated fats right – so when cooking use butter? Butter is better? I have heard that margarine is worse for you than butter (even if you have high cholesterol).
    Eat carrots, drink milk with honey, and use butter?

  5. ILONA KOZMA February 6, 2016 at 3:21 am - Reply

    thank you so much for all these advice

    • Tom Brimeyer February 6, 2016 at 7:18 pm - Reply

      Thanks Ilona for reading!

  6. Natalia February 16, 2016 at 6:43 pm - Reply

    Unfortunately, I also have interstitial cystitis and therefore cannot take either orange juice, or salt, or coffee… And my diet is mainly vegetables,including broccoli – I can eat only very few foods otherwise (eggs, quinoa etc.). What should i do then?

    • Tom Brimeyer February 17, 2016 at 11:31 am - Reply

      Hi Natalie, this is actually an important point of the article as your thinking about this quite backwards… Instead of focusing on the foods as the problem, what you need to do is correct the underlying problem. Then you’ll be able to tolerate the foods. Interstitial cystitis is a problem with estrogen dominance and a sensitivity to mast cells in the bladder. Regulating estrogen, thyroid, using broth/gelatin, etc. will help address the underlying problem. Even using a safe and proper antihistamine can relieve the symptoms temporarily.

  7. Brenda February 28, 2016 at 11:19 am - Reply

    Does this treatment plan work for Hashimoto’s? Hashimoto’s is supposed to be the cause of a large majority of hypothyroidism.

    • Tom Brimeyer February 28, 2016 at 11:31 am - Reply

      Hi Brenda, yes we address the underlying issues of hashimoto’s. It’s all interrelated.

  8. Stacy Shaw March 14, 2016 at 12:37 pm - Reply

    Thank you for your program! I have just started and am seeing small but noticeable differences in my energy level.
    I had my gall bladder removed 20 years ago. Does that throw a huge wrench into gut health issues? I have been hypothyroid for about 10 years.

    • Tom Brimeyer March 14, 2016 at 12:59 pm - Reply

      Hi Stacy, that’s great to hear. As for your gallbladder, that’s a common issue with estrogen dominance. If you don’t have any recurring issues related to it then it should be OK. If you have trouble digesting fats then lowering fat intake might be beneficial. And when needed bile salts can be helpful.

  9. Greg May 22, 2016 at 9:03 pm - Reply

    Tom, how do I proceed to find out if hypothyroid is causing my leaking gut syndrome?

    • Tom Brimeyer May 23, 2016 at 1:15 pm - Reply

      Hi Greg, as discussed in the article above, hypothyroidism and the resulting SIBO and endotoxin are all involved.

  10. nad June 16, 2016 at 1:24 pm - Reply

    Hi Tom,
    can I use the sunflower lecithin?
    Also very confuse w/gelatin-collagen – some rules on the net -take it on empty stomach, take it w/acid, what would you suggest?

  11. Jennie September 12, 2016 at 10:34 am - Reply

    I have Hashi’s and high cortisol levels which I am finding difficult to get down. Reading up above on fish oils and omega 3 etc, my Functional Medicine Dr prescribed me a OmegAvail which has a high EPA of 1000mg and EPA of 500mg. He wants me on 1 three times daily but reading the PubMed article I am not sure whether I should be having them now. I did have a stool test for leaky gut that came back negative but my Dr in the States (as I am in the UK) said the test probably wasn’t accurate. He said because I have Hashi’s I will have a leaky gut. Have never had any gut issues or food intolerances that I know about, but I do have undigested food particles in my stools. But saying that, since all my anxiety from my high cortisol, I do get a nervous stomach. Are you able to confirm whether I should be taking the OmegAvail or leave well alone? I do eat quite a bit of salmon and tuna. Many thanks

  12. Suhasini May 31, 2018 at 10:58 am - Reply

    It is my understanding that menopausal women have low estrogen levels. This should then be beneficial in hypothyroidism ? Why then do many menopausal women suffer with thyroid issues?

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