DEFINITION: Gut health refers to one’s entire gastrointestinal / digestive system, i.e your ability to properly digest your food and absorb nutrients. 

Why is Gut Health an important topic for us no matter the cause of our thyroid problem? Because the healthy function of your digestive system promotes better health. Conversely, an impaired digestive system can cause growing problems. 

And specifically for a large body of Hashi’s patients,  impaired gut health can both cause autoimmune problems as well as make the current autoimmunity issue worse!  

Check these out: 

1. Do I have the right amount of good bacteria in my gut?

Your digestive tract is meant to have billions upon billions of beneficial “good” microbes, aka bacteria, to help with digestion, immune system activity, mental health, and vitamin production like the B’s. But dysbiosis1 can occur, meaning one’s internal bad bacteria can increase over the good bacteria. Not only can dysbiosis cause or worsen autoimmunity problems in susceptible individuals like Hashimoto’s, it can also result in depression2, excess gas, diarrhea, intestinal pain, depression and more. There are even some genetic mutations causing too little amounts of certain good bacteria. (Janie Bowthorpe has a mutation that causes too little of the Bifidobacteria version of good bacteria). That’s why many people are using probiotic supplements which will vary by the bacterial strain, and will usually be anywhere from 1 to 10 billion CFU’s. Some recommendations state to vary the kind of strains you use. Another way to get more good bacteria is the consumption of fermented foods, which include kefir, greek yogurt, miso, sauerkraut or the fermented beverage called kombucha. Check out Chapter 10 about bacteria or dysbiosis in the informative book Hashimoto’s: Taming the Beast

2. Do I have Small Intestinal Bacterial overgrowth aka SIBO?

SIBO is a condition of having too much bacteria in the small intestine, believe it or not.3 That excess can interfere with the absorption of vital nutrients, besides cause uncomfortable digestive issues after eating certain carbs or high fiber…bloating in your stomach, chronic diarrhea, excessive gas or pain, nausea, or having the diagnosis of irritable bowel syndrome. Having SIBO might explain why someone with Hashimoto’s has trouble with high antibodies or difficulty getting them down!  The main two causes of SIBO appear to be having lowered levels of stomach acid or being underdosed even with desiccated or T3) or a slower rate of intestinal movement of food, called dysmotility or slowed motility. You can even get SIBO with a gallbladder problem causing low bile! How to find out if you have SIBO?? A breath test is one way to diagnose SIBO, or Organix has a bacterial dybiosis test a doctor can prescribe. Treatment is the use of the antibiotic Xifaxan via your doctor. Some doctors and patients are using alternative natural methods to lower the high bacterial count with garlic oil in capsules, wormwood, berberine, or other supplementsCheck out Chapter 10 about SIBO in the informative book Hashimoto’s: Taming the Beast

3. Do I have an enzyme deficiency which negatively effects my ability to break food down and thus get needed nutrients?

It turns out that there can be genetic mutations or inherited conditions causing one to not break down food correctly, thus missing out on having healthy levels of key nutrients. For some with Hashimoto’s, this can promote their autoimmune issues. Digestive enzyme deficiencies, or the inability to use enzymes correctly or even activate them, are a common reason for the failure to break down food well. How to know?? You can test elastace, amylase or lipase–the main pancreatic enzymes. There are excellent stool tests via prescription from your doctor that can reveal a problem. The symptoms of this problem can be silent, but one could see low nutrients in lab results, or in some….excess gas, bloating or cramping, heartburn, pain, or even nausea. This is where the use of digestive enzymes can help, or consuming bitters before meals to help promote enzymes. I, Janie Bowthorpe, have a rare deficiency of amylase–the digestive enzyme that breaks down starches/carbs. Thus I have to take amylase plus the medication called Creon. Check out Chapter 9, Hashimoto’s Gut Problem #1 about digestive enzymes in the informative book Hashimoto’s: Taming the Beast

4. Is my stomach acid too low to properly digest and absorb nutrients from food and supplements (due to still being hypothyroid)?

It’s all too common when undiagnosed or poorly treated hypothyroidism/Hashimoto’s to have low levels of stomach acid / gastric acid, medically called Achlorhydria or hypochlorhydria. The right amount of acid in your stomach is critical to both digest foods properly, plus to absorb key nutrients. Sadly, since low stomach acid cause cause acid reflux, a misdiagnosis can occur, thinking one has too much stomach acid instead of the reality of low stomach acid. The latter low stomach acid, as mentioned above, can lead to SIBO in some, or simply nutrient deficiencies in others. For Hashimoto’s patients, the lowered nutrients from having low stomach can promote autoimmunity, lower the ability to fight autoimmune issues, and/or make one feel bad. Check out Chapter 9, Hashimoto’s Gut Problem #2 about stomach acid in the informative book Hashimoto’s: Taming the Beast

5. Am I eating foods which exacerbate inflammation?

Bodily Inflammation can occur whether one has Hashimoto’s or not and for a variety of reasons, ranging from simply being poorly treated for hypothyroidism, to high heavy metals, to a sensitivity to gluten, to Celiac disease and more. For Hashimoto’s patients, inflammation is common when the thyroid is being attacked. But it’s a chicken or the egg situation, because inflammation also promotes one having autoimmune and more inflammatory responses!!4 Thus, it’s helpful to avoid or lower the consumption of those foods which might promote further inflammation and worsening symptoms. They can include most grains, dairy, nightshades, sugar, and even eggs…and any foods with gluten in them. Patients have reported that the GAPS diet had made a difference, as has an Autoimmune Paleo (AIP) Diet. Check out the patient-to-patient Chapter 13 about foods which patients have reported causing problems, plus Chapter 8 about inflammation, in the informative book Hashimoto’s: Taming the Beast

6. Do I need to avoid gluten-containing foods?

Granted, not everyone has issues with gluten, especially in moderation. It is false to state that “all” should avoid gluten. But the majority of Hashimoto’s patients reading this will see gluten causing a rise in antibodies as well as inflammation, just as they can see the removal of gluten lowering their antibodies and inflammation (even if some need extra methods to lower antibodies). Some can have the condition called Celiac referring to a damaged intestinal mucosa brought about by a inherited gene, while others just have an intolerance to gluten in general and reactions to match like chronic inflammation. Check out Chapter 9, Hashimoto’s Gut Problem #41 about the problem of gluten for the majority with Hashi’s in the informative book Hashimoto’s: Taming the Beast

7. Am I treating any and all causes of inflammation?

One common cause of Inflammation is either being undiagnosed hypothyroid, or poorly treated hypothyroid. For Hashimoto’s patients, gluten consumption is a major cause of their inflammation, and inflammation can be exacerbated by eating certain foods which promote inflammation, as explained in #5 above. Having high heavy metals or the detox can promote inflammation. Mold can promote inflammation. Whatever the cause, it behooves all of us who have inflammation to discover what the cause might be and treat it. This is important since chronic inflammation can promote autoimmune exacerbation via the pro-inflammatory cytokines released by your immune system4. And evidence shows that long term inflammation can be deadly. Check out Chapter 8, about the inflammation problem in the informative book Hashimoto’s: Taming the Beast

8. Is my liver healthy and helping me detox correctly?

When it comes to thyroid disease and liver, we are dealing with another chicken and the egg relationship. For one, many thyroid patients have known first hand that having undiagnosed hypothyroidism (due to the use of the faulty TSH lab test), or poorly treated with T4-only, can lead to liver stress and even fatty liver disease5, i.e. too much fat around the liver. But can liver problems promote health problems or even autoimmune issues like Hashimoto’s? That’s a possibility. Your liver in your primary detox organ. So if it’s not optimally detoxing those toxins or excess heavy metals that you are exposed to, or those elevated heavy metals from an active MTHFR mutation, that could potentially flair one’s autoimmunity tendencies. So how to make your liver more healthy? For one, there are great supplements to promote healthier liver function, ranging from Milk Thistle to Dandelion Root. Eliminating processed foods is important, as well as eating healthy foods. Regular exercise is said to promote a healthy liver, as well as maintaining a healthy weight. By the way, the two most revealing lab tests for the health of your liver are the ALT and AST. And Janie Bowthorpe has noted frequently over the years that those people with healthy livers have those two latter test results in the teens. Check out the informative book Hashimoto’s: Taming the Beast with several mentions about liver health.

9. Do I have parasites in my gut that need discovery and treatment?

Ick. It’s not a fun thought to think we might have parasites in our intestines creating autoimmune problems or even simply a rise in the antibodies we already deal with. But it’s very possible. Here’s a case of a man who had Blastocystis hominis parasites, and once treated, his Hashimoto’s antibodies went down!  Symptoms of a parasitic problem can be silent, or one can have soft stools, diarrhea, bloating or anal itching, to name a few. Most doctors will do a stool test, and the Centers for Disease Control recommend you do it three or more times.  If parasites are present, your doctor will whip up an anti-parasitic treatment. Check out Chapter 10 about the icky parasites in the book Hashimoto’s: Taming the Beast.

10. Do I have a leaky gut?

It’s proposed that that all those epithelial cells which line your intestines could acquire too-large spaces between them, technically called intestinal permeability. Thus, your intestinal walls become “leaky”, meaning certain toxins and bad bacteria can get into your blood. The latter situation can create problems in your health. Or even in those susceptible, can push someone into having Hashimoto’s disease, or cause your already-present antibodies to go even higher as your immune system over-responds. How does one potentially acquire a leaky gut? The main cause seems to be chronic inflammation, such as via Celiac disease, severe gluten intolerance, irritable bowels, or Crohn’s disease…or any condition causing chronic inflammation, which was mentioned in #7 above. Even excess alcoholic drinking could promote a leaky gut, or damage caused by parasites. What are potential symptoms of having leaky gut?  Being hyper sensitive to certain foods can be one, as can be having diarrhea, rashes on your skin, fatigue, headaches and more. Another clue is testing your nutrients and finding them low. Check out Chapter 10 about leaky gut in the book Hashimoto’s: Taming the Beast.

Stop the Thyroid Madness now has a life-changing companion book to the original classic Stop the Thyroid Madness, called Hashimoto’s: Taming the Beast

It’s written in a way to be easier to get through without long stories or chit chat. Each chapter even has a NOTES section for you to refer to your favorite pages or other information!

You can read more about it here, and even order it here.

Need to order your own labwork? Scroll down on this page: 


Important note: STTM is an information-only site based on what many patients worldwide have reported in their treatment and wisdom over the years. This is not to be taken as personal medical advice, nor to replace a relationship with your doctor. By reading this information-only website, you take full responsibility for what you choose to do with this website's information or outcomes. See the Disclaimer and Terms of Use.