It’s very common for people with hypothyroidism to continue to struggle with fatigue, brain fog, weight gain and other symptoms of hypothyroidism, despite taking a synthetic thyroid hormone such as Synthroid or levothyroid. It’s also common for practitioners to attempt to address unresolved symptoms by adjusting the dose or changing to another type of thyroid medication.
But tinkering with thyroid medications when you have gut inflammation or a gut infection is not likely to improve your symptoms. It’s like adding gas to your car when the battery is dead. Here is a four-step process that I use with thyroid patients to ensure that we fully address the root causes of symptoms and also personalize thyroid medication requirements.
There are risks associated with the supplementation of T3, so I save this step for last. Most patients don’t need to take additional T3.
Once you have a diagnosis of hypothyroidism, your practitioner may become completely focused on finding the right pill to get your TSH (thyroid-stimulating hormone) in range. This very common approach completely overlooks the profound importance of the gut-thyroid connection and minimizes the significance of your symptoms.
If you have thyroid disease or low thyroid function, it’s important to know that:
Correcting imbalances in the gut may decrease thyroid autoimmunity. Autoimmune thyroid (Hashimoto’s disease) is the leading cause of hypothyroid symptoms.
Some hypothyroid-like symptoms are caused by inflammation in the gut. This is not true hypothyroid and can be corrected with better gut health. In this case, taking thyroid medication won’t improve your symptoms.
For some patients, poor gut health impairs the absorption of thyroid medication. Healing the gut will help your medications work better.
Thyroid hormone replacement alone is not likely to resolve your thyroid symptoms if you have gut inflammation or a gut infection.
The Thyroid-Gut Connection
Preliminary research suggests an association between autoimmune thyroid disease and poor gut health.
One small study found that SIBO patients were more likely to have impaired thyroid function (as shown by blood tests) than healthy controls. 
In a much larger study, 1809 patients with SIBO were screened for co-existing health conditions. Hypothyroidism or take synthetic thyroid hormone medications were the conditions most highly associated with SIBO. 
A meta-analysis of 7 studies (862 patients) explored the connection between H. pylori infection and autoimmune thyroid disease. The study found a significant association between H. pylori (a bacterial gut infection) and Graves’ disease but no significant association for Hashimoto’s disease. 
Preliminary evidence also suggests that GI treatment can improve thyroid autoimmunity, reduce symptoms and result in decreased thyroid medication dose.
A small but promising study found that treating H. pylori infections can improve thyroid autoimmunity.  Patients treated for H. pylori had an average drop in TPO antibodies of 2029.
The Journal of Infection in Developing Countries published a case study involving a 49-year-old man diagnosed with Hashimoto’s disease and Blastocystis hominis (a parasitic infection of the gut). 
A two-week antiparasitic treatment eradicated the gut infection and also fully resolved the man’s symptoms of chronic rash and swelling.
In four years of follow-up testing, thyroid hormones were normal, thyroid antibodies declined and symptoms did not reappear.
Autoimmune thyroid and poor gut health are very likely associated.
Thyroid Symptoms or Gut Symptoms?
Patients typically think of symptoms like fatigue, brain fog, depression and anxiety as symptoms of hypothyroidism. But there’s good evidence to show that all of these are also symptoms of poor gut health. For example:
A survey of 160 IBS patients found that fatigue occurs in a sizable proportion of IBS patients. Depression and anxiety were also common symptoms.
A meta-analysis of 17 studies found that more than 50% of IBS patients have symptoms of fatigue. 
Another meta-analysis reviewed 10 clinical trials (1349 patients) and found that treating the gut with probiotics can result in significant improvements in the mood of individuals with mild to moderate depressive symptoms. 
A further study showed that treating leaky gut reduces fatigue and other symptoms in patients with chronic fatigue syndrome. 
2 more studies show that treating the gut with a low FODMAP diet improves fatigue in those with IBS and fibromyalgia. , 
Stubborn symptoms of hypothyroidism that do not resolve with thyroid medication may, in fact, be symptoms of poor gut health. This is great news if you are a thyroid patient who struggles with unresolved symptoms.
Your Gut May Not Be Absorbing Your Thyroid Medication
Imbalances in the gut can cause malabsorption of thyroid medication. This is another reason that we prioritize healing the gut for those with thyroid issues. Here’s relevant research:
2 studies showed that lactose restriction and a gluten-free diet led to significant decreases in TSH levels for patients taking synthetic thyroid hormone. The authors of both studies suggest that food sensitivities like lactose and gluten intolerance can lead to impaired absorption of thyroid medication. , 
3 studies have found patients who treated H.Pylori experienced improved TSH levels., ,  Some of these patients needed a lower dose of thyroid medication after being treated.
Heal your gut and you may need to reduce your thyroid medication.
Thyroid Medication is Overprescribed
For some patients, minor fluctuations in thyroid lab results may be caused by gut imbalances. Far too many practitioners leap to the hypothyroid diagnosis based on mildly abnormal blood test results.
Research suggests that thyroid medication is overprescribed:
One very insightful study  paused levothyroxine treatment for 6-8 weeks in a group of 291 patients. Many of these patients had been taking thyroid medication for years but did not have strong diagnostic indicators of thyroid disease.
After going without synthetic thyroid hormone replacement for several weeks, 60.8% of patients had normal lab results.
60% of these subjects did not require thyroid medication.
These patients were able to discontinue their thyroid medication, without any health interventions.
In my experience, a small percentage of ‘thyroid patients’ will discover that their TSH levels completely normalize once their gut issues (gut infections, intestinal permeability, imbalances of the microbiome, etc.) have been treated and they can discontinue thyroid medication. Other patients do need to continue with thyroid hormone replacement and, after healing the gut and reducing symptoms, can more easily optimize their medications.
By following a logical hierarchy for the treatment of hypothyroidism, it’s possible to sort out the true cause of your symptoms.
Four Steps to Thyroid Health
Let’s explore each of the four steps in greater detail.
STEP 1 – Standard T4
1a: Standard T4 trial, with dose adjustments
Is the patient missing doses?
Is the medication being taken on an empty stomach?
1b: Optimize gut health & general health
Our first step is to stabilize TSH levels while taking steps to heal the gut, improve diet and lifestyle and reduce symptoms.
It’s best to start with a standard T4 medication like Levothyroid or Synthroid and use blood tests to monitor TSH levels. As a patient’s health improves and symptoms start to resolve, we may actually need to lower the T4 dosage.
And while gut health is very important, we also want to assess overall health and lifestyle at this point. In my observation, the most common causes of non-responsiveness to synthetic thyroid hormone are:
Lack of sleep
Gut imbalances such as IBS, SIBO, dysbiosis, H. pylori, etc.
Female hormone imbalances
Addressing diet, lifestyle and gut health will improve the health of the patient, resolve symptoms and potentially reduce medication dosage.
Many patients have no need to take further steps after completing Step 1. For others, it will become apparent if further steps are required.
STEP 2 – Increase T4
2a: Screen for/treat low ferritin
2b: considerably higher than normal T4 dose
If thyroid patients are still not feeling better after Step 1, I like to check ferritin levels. Ferritin is a simple test that shows if your body’s iron stores are low. Low iron can cause fatigue and other symptoms and is often overlooked.
A common cause of low ferritin is low stomach acid. This can cause malabsorption of dietary iron (and can lead to malabsorption of your thyroid medication too). If you have Hashimoto’s disease, there’s a 20-30% chance that you also have low stomach acid. 
One researcher has documented that women with hypothyroidism who are on medication and still not feeling well can improve symptoms by getting their ferritin level over 100 with iron supplementation. 
If your ferritin levels are low, you can also take a trial of supplementary HCI to increase your stomach acid and improve iron absorption.
Increasing T4 dosage is a conservative way to boost T3 production. This is a far safer choice than combined T3 and T4 hormone replacement and works for many people.
Common advice suggests that a combination of T4 and T3 hormones is better than T4 alone. The rationale for this advice goes like this:
T4 must be converted to T3 before your body can use it.
Much of this conversion happens in the liver.
Some people are less efficient at converting T4 to T3.
Therefore, you need to supplement with T3.
However, the evidence does not back up this advice.
A meta-analysis of 11 studies with 1219 patients showed no evidence that combined T4/T3 is a better alternative to T4 therapy alone. 
Some patients have adverse reactions to T3 hormone, including cardiovascular symptoms. T3 may be risky for patients with cardiovascular disease.
Side effects from too much T3 include:
Racing heart or palpitations
T4 hormone is far less likely to cause side effects, even at higher doses.
Once again, we are adjusting medication while tracking symptom improvement and blood test results. Generally, I like to see a TSH reading in the lowest 1/2 of the recommended lab range.
STEP 3 – Alternative T4
3: Depending on patient history and context:
Consider a trial of hypoallergenic alternative (Nature Throid, WP Thyroid)
Consider a trial of liquid T4
Some patients have issues with standard T4 medication. There are a few things we can try next:
Occasionally we see excellent blood test results with T4 hormone, but the patient still has symptoms. Symptoms may be caused by fillers and binders in medication. So, we might try a hypoallergenic tablet such as Nature Throid or WP Thyroid and see if the symptoms resolve.
Even with improved gut health, some patients still have absorption issues. Some patients do better on liquid T4. One study showed that patients with prior H. pylori infections respond much better to liquid T4. 
STEP 4 – Add T3
4: Consider trial addition of T3
Finally, if we are still not getting the results we want, we can try adding T3.
There are some patients that do better with added T3. But they are not the majority. They may even be a significant minority. Since there are risks with T3 hormone replacement, we follow symptoms and blood test results closely and make dosage adjustments as needed.
It’s very gratifying when a patient’s symptoms completely resolve once their gut health is optimized.
A great example of this is Laura’s story. After taking simple steps to improve her gut health, Laura was able to cut her dose of synthetic thyroid hormone in half. Even more exciting, her symptoms of fatigue, insomnia and fuzzy thinking completely cleared up and she lost weight.
Thyroid practitioners and patients can easily miss opportunities for significant health improvements when they are too narrowly focused on finding the right thyroid medication. Start with the fundamentals of diet, lifestyle and a healthier gut!
Bertalot G, Montresor G, Tampieri M, et al. Decrease in thyroid autoantibodies after eradication of Helicobacter pylori infection. Clin Endocrinol (Oxf). 2004;61(5):650‐652. doi:10.1111/j.1365-2265.2004.02137.x
Livadas S, Bothou C, Androulakis I, Boniakos A, Angelopoulos N, Duntas L. Levothyroxine Replacement Therapy and Overuse: A Timely Diagnostic Approach [published online ahead of print, 2018 Nov 30]. Thyroid. 2018;10.1089/thy.2018.0014. doi:10.1089/thy.2018.0014
Rayman MP. Multiple nutritional factors and thyroid disease, with particular reference to autoimmune thyroid disease. Proc Nutr Soc. 2019;78(1):34‐44. doi:10.1017/S0029665118001192
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