Gut problems and intestinal problems are common issues for people with thyroid disease including Hashimotos and Graves Disease. This article reviews the “10 Most Common  Gut and intestinal Problems Seen In Patients with Hashimotos and Graves DiseaseIn the 20 plus years, I have been practicing and working with patients with Thyroid problems, these are the most common Gut/intestinal problems I see on a daily basis in those patients.  The other thing I can tell you is that whether you have Hashimotos disease, Graves disease, Hypothyroidism or Hyperthyroidism, you will never correct or stabilize your thyroid autoimmune condition until these have been addressed. That’s how important this is!

Alright, so let’s get into these, First I will tell you what they are and then I will explain each one and their importance in thyroid and autoimmune disease and like I said if you want more information on any of these, I will leave a link in the description of today’s video to the page where you will find the transcript.

The 10 Most Common Gut and Intestinal Problems Seen In Patients With Thyroid Disease Including Hashimotos And Graves Disease

  1. Gut Dysbiosis
  2. Leaky Gut
  3. Food Sensitivities
  4. Small Intestinal Bacterial Overgrowth
  5. Low Stomach Acid
  6. Yeast or Fungal Overgrowth
  7. Fat Malabsorption
  8. Inflammation in the gut
  9. Low SIgA
  10. Low SCFA and low gut bacterial diversity (these two kind of go together)

One thing I can promise you is that if you have any of these intestinal and gut imbalances (that you are going to learn about today) and you identify them and work on correcting them, I promise that your health with skyrocket more than any drug a doctor could prescribe to you and your health will improve in more ways than one.

You Can’t Fix A Thyroid Problem, If You Don’t Know What Kind Of Gut Problem You Are Dealing With.

#1 Gut and Intestinal Problems Seen In Patients With Thyroid Disease and Hashimotos – Intestinal Dysbiosis 

So, we have a vicious cycle going on here. On one hand, Low thyroid function can lead to gut dysbiosis and on the other hand, gut dysbiosis can suppress thyroid function and lead to an autoimmune condition called Hashimoto’s Thyroiditis.

It’s hard to imagine, but right now you are carrying around approximately 4-5 pounds of bacteria in your colon.

Your gut microbiome is home to hundreds of varieties of bacteria, which are specific to the human body and unfortunately 70 million Americans suffer with some sort of Gut problems in which they are making their gut unhealthier by all the medications and antibiotics they are taking to treat the symptoms.

Because the lining of your digestive system is loaded with all kind of immune system cells, and those immune system cells are part of an important barrier, poor gut health can be a significant Trigger in the development of an autoimmune disease including Hashimotos disease, Rheumatoid arthritis, MS, Type I diabetes, Inflammatory bowel disease like Crohn’s and Ulcerative colitis and many metabolic conditions.

Boosting Thyroid Function- Gut Dysbiosis

A Few weeks ago, I did a video on “How to boost thyroid function by 60%”: it was a two part video series where I talked about the role the liver plays in converting T4 into T3, I talked about how to support the liver and many other topics related to the connection between your liver and your Thyroid, but the liver is not the only place T4 to T3 conversion takes place. One thing I didn’t talk about in the past video was just how important the gut microbiome is to thyroid health. It turns out that the liver is not the only place where this T4 to T3 conversion takes place.

Another 20% of thyroid hormone conversion occurs in the intestines, but only if you have the right kinds of bacteria and if you are not dealing with gut dysbiosis. If you have gut dysbiosis you will make less T3 hormone and this will cause all the hypothyroid symptoms like fatigue, weight gain, anxiety, depression, hair loss, feeling cold all the time.

You see, beneficial bacteria in the gut are not only needed for the conversion of T4 thyroid hormones into T3 thyroid hormones, but these gut bacteria also play a major role in the modulation of both Th1, Th2 and Th 17 immune responses and this is the connection the gut microbes and autoimmune diseases.

These Imbalances between Th1, Th2 and Th17 immune responses, is what is now understood to be one of the major causes in the development of autoimmunity.

So, if you are following along with me here, it should makes sense that If you can identify those things that shift the balance of Th1 and Th2 and Th17 you are going to stabilize an autoimmune disease and perhaps put this disease into remission and that’s going to help you feel better and get your life back!

4 Things to Remember About Thyroid and Gut Function

There are Four main things that I want you to think about when it comes to the link between thyroid function and gut function and why if you have a thyroid or autoimmune disease why you would benefit from testing and digging deeper into this understanding of thyroid-gut health connection.

#1 the majority of your immune system cells are located in the gut mucosal lining. So at the end of the day, regardless of what kind of thyroid problem you have, you really want a healthy mucosal lining.

#2 I already said this, but it’s worth repeating, the gut is a major area where conversion T4-T3 occurs

#3 Bacteria found in our gut, participate in the production of many vitamins, that are so important to that Th1,Th2 and Th17 immune response, additionally

#4 deficiencies in these vitamins are common and Ironically these vitamin deficiencies perpetuate immune system dysfunction and a loss of mucosal tolerance.

For just a moment think about the implications this has on people who have autoimmune disease like Graves, or Hashimotos disease.

If you have gut dysbiosis, you won’t have the proper bacteria in your gut that you need in order to make vitamins such as your B vitamins, vitamin K, vitamins A and D and all of the others needed for Thyroid health.

While I have done videos on the common nutritional deficiencies  and how they relate specifically to thyroid and immune function, it easy to say that correcting gut dysbiosis will be a huge advantage to improving thyroid function and vitamin status.

Problems #2 and #3 Gut and Intestinal Problems Seen In Patients With Thyroid Disease and Hashimotos- Leaky Gut Syndrome and Food Sensitivities

10 Of The Most Common Gut and Intestinal Problems Seen In Patients with Thyroid and Hashimoto's Autoimmune Disease

These problems are very intimately connected. Leaky gut has gained a lot of attention in the last five or 10 years and for good reason.

Leaky Gut also known as intestinal hyperpermeability is another major problem to those with Autoimmune diseases as well at thyroid disease. Earlier I mentioned the important of the gut barrier to immune function. If you look at this picture

when this barrier breaks down, it allows toxins, bacteria, etc to enter bloodstream where they now come in contact with and provoke an immune response. Your immune system is constantly patrolling your body and what is in it.

Moment to moment from the air you breath in, to food you eat, to the medications you take, your immune system is making a decision real time as to whether or not something is a friend or foe.

These foreign invaders have the potential to weaken these tight junctions and slip on by. These invaders might be things like undigested food proteins. Things like casein, whey and butyrophilin- If you have never heard of these before these are the proteins you find in milk, butter, cheese, you’re your whey protein shakes)

In individuals who test positive for these proteins, these are going to have an adverse effect on your  thyroid and immune function.

Other food proteins found to be problematic to the immune system especially when you have a leaky gut include the proteins found in Gluten, Soy, Corn, Eggs and Yeast to name a few.

From an environmental and chemical standpoint, It has been shown that certain household toxins  found in our plastic containers and in our soaps, shampoos, deodorants, and detergents can play a role in triggering autoimmunity. These are going to be things like phthalates, Bisphenol A, and Parabens.

Research has also shown that exposure rates to certain heavy metals such as mercury, cadmium, Tin, Arsenic and Lead is much higher than expected and these heavy metals poses a very serious threat to our immune system and can trigger various autoimmune diseases including Hashimotos disease and thyroid problems.

There’s More To Leaky Gut……

In a past video, I reviewed what causes a leaky gut, how to properly test for leaky gut, and conditions that have been associated with a leaky gut. So, again if you want to know more about leaky gut I have plenty of information on that topic for you.

So, the takeaway here, is that by discovering and addressing what you, are immunologically reacting to (food sensitivity, chemical sensitivity), etc…can help you not only make massive changes in your dietary choices but also, eliminate your exposure to chemicals.

That information can be one of the most powerful lifestyle interventions and steps you can take towards better thyroid function and immune stabilization.

Think about it like this, if you knew your immune system was reacting to parabens, pthalates or plastics, or to dairy, whey, casein, or you had high levels of mercury and arsenic, I would guarantee you that you would make a very conscious choice of removing all the potential autoimmune triggers at your workplace, and your home. Information is power and without knowing what is triggering your thyroid and autoimmune disease, how could you support or stabilize the immune system.

# 2 Food sensitivities and

#3 Leaky gut.

Problem #4 Gut and Intestinal Problems Seen In Patients With Thyroid Disease and Hashimotos- Small Intestinal Bacterial Overgrowth or SIBO

How SIBO Contributes to Hypothyroidism

The next intestinal problem we see on a daily basis in people who have Thyroid disease and Hashimotos is an overgrowth of gram-negative and gram-positive bacteria in the Small intestines known as SIBO.

Normally, the small intestines is not home to these bacteria. However, with SIBO, bacteria in the large intestines migrate up into the small intestines due to dysfunction in the ileocecal valve.

When these bacteria take up shop in the small intestines, the symptoms are identical to IBS you get the bloating, abdominal pain and cramping, gas, constipation or diarrhea.

If you notice these symptoms when you eat fiber, starch, carbohydrates, sugars, then you might be suffering from SIBO.

If you visit my website, on the right-hand side at the top you will see a section where is says “Quizzes” under quizzes you will see SIBO Quiz. This quiz will go through some of the most common symptoms and signs of SIBO and when you are all done it will tally up your score and determine your risk level for SIBO.

The other thing about SIBO I want you know about is that many people with Thyroid disease have SIBO or will go on to develop SIBO because of thyroid medication and Yes you heard me say that. Thyroid medication can cause SIBO!

Take a look at this study from “World Journal of gastroenterology” This study released in 2017, If you look at the conclusion, it states “The most important contributors for the development of SIBO was a compromised immune system, impairment of intestinal clearance which is slow motility and finally levothyroxine use.”

If you are interested in learning more about SIBO, you can watch a video I did titled, “SIBO and its connection to Thyroid Disease”

That’s #4 when it comes to the 10 types of intestinal problems seen in patients with Thyroid disease and Hashimotos.

Problem #5 Gut and Intestinal Problems Seen In Patients With Thyroid Disease and Hashimotos- Low Stomach Acid and or H.pylori

gut and intestinal problems

Unfortunately, for people with Thyroid disease and Hashimotos another common gut intestinal problem that I see frequently is Low Stomach Acid or an infection of H.pylori.  And again, when someone has low production of stomach acid, you are more vulnerable to an infection with H.pylori.

Hypothyroidism can lead to hypochlorhydria which is the term given when the stomach fails to produce sufficient amounts of stomach acid.

For many people with Hashimotos, research shows about 1/3 of them can develop antibodies against the cells that not only produce stomach acid, but also against something called intrinsic factor.

Intrinsic factor allows you to absorb vitamin B12, and what do we know about B12 and thyroid disease?

We know that most people with Hashimotos and Hypothyroidism have low B12 levels

Now, I want you to listen very carefully about what I am about to tell you, because this is very important.

If you have low B12 levels or low Iron levels or low zinc levels and you have a history of Depression or other mental health problems, your doctor should be on the lookout for a condition called atrophic gastritis and pernicious anemia- this too is an autoimmune disease that commonly shows up when someone has hashimotos. So just be aware of that and discuss that with your doctor.

But coming back to low stomach acid, low stomach acid creates several problems for people with thyroid disease- If foods (especially proteins) are not properly digested due to insufficient stomach acid production, that protein putrefies and becomes rancid in the stomach and you will most likely develop symptoms of frequent bloating, belching, burping, GERD and acid reflux.

While there are many other causes of low stomach acid, what is more troublesome is how insufficient stomach acid creates a snowball effect of problems in the lower GI tract.

Because of the insufficient stomach acid, the contents of the stomach are not properly sterilized so we can also develop bacterial infections like H.pylori in either the stomach or in intestines.

Another consequence to low production of stomach acid is that the gallbladder doesn’t release sufficient amounts of bile to help absorb all those good fat soluble vitamins that we need for proper Thyroid health and Th1, Th2 and Th17 immune response. As a result we end up with deficiencies in vitamins A, D, E and K Are your vitamin D levels low on regular basis? Less than 50? If so, that’s a problem!

Again, because of insufficient stomach acid production, the small intestines can’t properly digest the rotting proteins, and this leads to inflammation, it leads to that leaky gut we just talked about, it leads to gut dysbiosis, it lead to that debilitating fatigue after a meal, food allergies and small intestinal bacterial overgrowth.

Essentially, what we have is a cesspool that needs to be sterilized, but with insufficient production of stomach acid, protein, starch and fat digestion comes to halt.

This is one of many reasons Thyroid sufferers struggle with repeat SIBO, Yeast and H.pylori infections.

Problem #6 Gut and Intestinal Problems Seen In Patients With Thyroid Disease and Hashimotos- Yeast or Fungal Overgrowth-

Candida and Yeast Testing

Another common GI problem I frequently see in my patients with thyroid disease is yeast and fungal overgrowth.

Many times, with dysbiosis, various strains of yeast like candida albicans become dominant in the gut, and essential they take over and overwhelm the good bacteria. This is called Fungal Dysbiosis and it can sometimes accompany Small Intestinal bacterial overgrowth.

With yeast overgrowth, symptoms can vary from person to person but the most common symptoms include sugar cravings, fatigue, depression, headaches and brain fog and sometimes the sensation of feeling hung over.

Remember that yeast can produce over 100 different toxins and this is why we see so many different kinds of symptoms associated with yeast overgrowth.

If you suspect a yeast overgrowth, you can visit my website and look for the Candida quiz. Go through and answer the questions and when you are all done submit your questionnaire.

Within just a few minutes, you will get an email with your score indicating the risk or likelihood of a fungal overgrowth and our recommendations of what you should do next. That is #6 on our top 10 list of most common intestinal imbalances seen in patients with thyroid and Hashimotos disease.

Problem #7 Gut and Intestinal Problems Seen In Patients With Thyroid Disease and Hashimotos- Fat Malabsorption and Gallbladder disease

People with Hashimoto’s and hypothyroidism often experience fat malabsorption as well as gallbladder disease.

Some studies show that as much as 50% of the people who are diagnosed with thyroid disease also have IBS. Liver function and gallbladder function are essential for the breakdown of fats. However if these fats are not properly broken down, you may be suffering with fat malabsorption.

Here is an example of a patient of mine who suffers with fat malabsorption. What you see here is that all of his levels are in that 5th quintile distribution.

gut and intestinal problems


His triglycerides high, long chain fatty acids- High, Cholesterol is high and the top marker that says Pancreatic Elastase 1 says 185. I know it says >200 but Health levels are over 500. For this patient this has created major digestive problems.

Fat malabsorption means fat soluble vitamins like ADEK as well as the good fats you should be eating from foods like fish, avocado, olive oil, coconut oil are going to not get properly absorbed.

In additional to Fat malabsorption, many of my thyroid patients have gall bladder problems or they have had their gallbladder removed.

If your gallbladder is not functioning optimally due to thyroid disease, your bile which is made in the liver and helps you breakdown fats can become saturated with cholesterol, this cholesterol can then crystalize and form gall stones. When the stone get big enough they can block your bile ducts causing gallbladder disease.

The other problem we see is that when bile flow is decreased, peristalsis is slowed down. Peristalsis are the wave-like muscle contractions that propel food, bacteria, waste through the intestines. If peristalsis is reduced, you will develop constipation and with constipation you could then develop SIBO.

Hopefully what you are starting to see is how many of these gut and intestinal problems, (so common in thyroid disease are all connected)- this is why using medication to treat the symptoms, only makes all of this worse.

gut and intestinal problems

If you don’t get to the root cause these problems and identify them you wind up dealing with multiple problems at the same time and by the time most people finally reach out to me, that’s what is happening. So keep in mind taking medications for these problems is like sweeping the dirt under the rug, at some point in time, you need to pick up the rug and deal with all the dirt. That is #7

Problem #8 Gut and Intestinal Problems Seen In Patients With Thyroid Disease and Hashimotos- Inflammation.

Inflammation, Autoimmune disease and thyroid disease go hand in hand. At the root of Hypothyroidism and Hashimoto is inflammation.

Inflammation is your thyroids worst enemy and here’s why….Inflammation can suppress the feedback loops between your brain and your Thyroid. By suppressing the feedback loops, you have less TSH circulating in the blood.

Less TSH means less of a signal going to your thyroid which can show up as less Thyroid hormone production.

That’s the first problem, the other problem is that inflammation causes an increase in Reverse T3.

Reverse T3 is different than the T3 your thyroid makes, but it is similar enough to bind to the receptor sites that are designed for T3.

So, what happens is, that High levels of Reverse T3 competes with T3- This leaves you in a low thyroid state.

It is two part video series and I explain some of the inflammatory markers I like run on my patients with Hashimoto disease, the cause of inflammation, supplements to help with inflammation.

Problem #9 Gut and Intestinal Problems Seen In Patients With Thyroid Disease and Hashimotos- SIgA levels

Chances are you probably never heard of Secretory Immunoglobulin A (Secretory IgA, or SIgA for short) But secretory IgA is especially important for individuals who have Hashimotos disease or are dealing with multiple autoimmune diseases.

Mucosal surfaces cover a large part of our body. The digestive tract, nose, mouth and throat are prime examples where this mucosal layer plays a critical role in supporting our immune systems health.

These mucosal surfaces of your body are the first line of protection against invaders and these surfaces are equipped with specialized cells, called B- cells.

These B- cells produce SIgA. Having High or low secretory IgA levels is a sign of compromised immunity especially when levels are low.

Here is an example of a patient of mine who we originally tested back on 5-20-2018 for SIgA Levels

What you will notice here is that his levels were incredibly low at 130.

Over the next 12 months, we worked a lot with this patient to correct his gut health- we worked on diet, we worked on leaky gut, we worked on various vitamin levels, we worked on food sensitivities, Oxidative stress, we worked on gut dysbiosis, we worked on inflammation, we cleared some of his parasites.

Here is his post test, and you can see that these levels improved drastically. But we had a lot of work to do with this patient.

Notice that his levels went from 130 ug/g which is very low to 1625 ug/g- which is exactly where I like to see them- They are right in the middle range. This is a good robust and strong level.

This is a great sign that the immune system is getting stronger and more stabilized.

Now, there are many things that can affect your SIgA levels and the more things you understand behind the cause, the better your chances are at correcting the problems, You can’t fix what you don’t know.

So low SIgA levels is #9 on our list of most common intestinal imbalances seen in patients with Thyroid disease and Hashimotos.

Problem #10 Gut and Intestinal Problems Seen In Patients With Thyroid Disease and Hashimotos- Low Levels of Bacterial Diversity and Low Levels SCFA-

Another major problem seen in patients with Hashimotos disease and Thyroid disease at it relates to gut health is low levels of Short chain fatty acids as well as a reduction in gut bacterial diversity and these often go hand in hand which is why I put them together.

SCFAs like butyrate are produced by the gut microbiota during the fermentation of starches and carbohydrate and they are some of the most powerful gut signaling compounds which have been shown to have a tremendous impact on brain health, hormones, immune function, cardiovascular function and even insulin resistance and weight gain.

There is now an abundance of research to show that short-chain fatty acids (SCFAs) play an important role in the maintenance of health and the development of disease.

Unfortunately, while Ketogenic diets and AIP diets can be incredibly helpful to those patients who have Hashimotos and thyroid disease, what we often see as a result of these diets is reduction in microbial diversity along with low levels of short chain fatty acids. And that’s because these diets limit fruits, nuts, grains, seeds and various vegetables that are high in fiber and are known to increase Short chain fatty acid levels.

As you can see from this test that I ran on a patient, this patient had low levels of SCFA and this created some unique challenges because this patient not only has Hashimotos disease but this person also has Small Intestinal Bacterial Overgrowth.

People with SIBO or small intestinal bacterial overgrowth, can’t tolerate fiber, fruit, sugars or starches, in fact, the more fiber, starches and fruits you give to this person, the more you feed the gut bacteria and cause even greater bacterial overgrowth.

So, for people who have both SIBO and Hashimotos, it becomes a vicious cycle.

Ultimately, the person needs fiber and starches in order to increase gut microbial diversity and improve SCFA but you can’t feed the bacteria either because in doing so, you create more dysbiosis which in turn can adversely affect thyroid and immune function.

Short chain fatty acids are some of the most powerful gut signaling compounds and they have a tremendous impact on brain health, hormones, immune function, cardiovascular function and even insulin resistance and weight gain.

When microbial diversity is reduced, it is also common to see low levels of short chain fatty acids.

If you are someone who suffers with insulin resistance, weight gain, prone to storing fat rather than burning it, you might be having problems with low microbial diversity and low levels of short chain fatty acids.

Treatment Options When You Have A High TSH 1

So, If you hung in there for all 10 types of intestinal imbalances seen in patients with Thyroid disease and Hashimotos disease, I am super proud of you!

I hope this video helped explain why you are still struggling with Thyroid disease or Hashimotos and why you may not be where you want to be with your health.

I wish I could tell you how to treat each of these conditions I talked about today, but it is much more complicated then changing your diet and take X, Y, Z supplements for this condition or that condition.

When getting to the root cause of your problem there are no short cuts and there are no cookie cutter protocols than you can follow from the internet or from a Facebook group and this is why you need to work with an experience functional medicine practitioner and get the proper testing. Facebook groups are the blind leading the blind.

Finally- keep in mind that chronic health problems are complex, there are many layers and the more pieces of your health puzzle you have uncovered, the easier it will be to understand how this all fits together and ultimately help you achieve incredible health. That I can promise you!

I hope that you will subscribe to my YouTube Channel, I’ll see you again….. take care

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