This article was written by Dr. Lindsey Berkson and is shared here with her permission. It originally appeared on her Substack: Agile Thinking. You can find the original article here.
Dr. Berkson is a respected voice in functional and integrative medicine, known for her deep dives into the science behind hormone and gut health.
At Synergetics Health in Las Vegas, we see the thyroid gut connection every day in our work with autoimmune clients. For those struggling with Hashimoto’s or unexplained low thyroid symptoms, improving gut function can often be the missing link in lasting relief.
That’s why we’re sharing this important article with our readers and patients. The research is clear, and Dr. Berkson’s perspective matches our own experience in the clinic: you can’t heal the thyroid without understanding what’s happening in the gut.
Low thyroid function = gut biome issues? Much of autoimmunity starts in the GUT!
In functional medicine we say many autoimmune diseases starts in the gut.
Over time, being in the “biz” for so long, it’s apparent that often functional perspectives first laughed at, completely disrespected, turn out later to be embraced as fact.
While too many patients miss out.
Now we see this with the gut/autoimmunity connection.
We have a study proving this with the thyroid/gut cross-talk, or Thyroid/Gut Axis.
In functional medicine we often say autoimmune diseases, like Hashimoto’s (autoimmune issues with they thyroid), MS (autoimmune issues with the insulation around nerves, RA (autoimmune issues in joints) and on and on, start in the gastrointestinal tract.
This means looking at all aspects of the gut, from the biomes (all throughout the digestive tract starting in the sinuses and heading southerly), to the gut wall’s ability to “open” and “close” optimally, to the functionality of the gut immune system called secretory IgA or SIgA.
A study now demonstrates a link with autoimmune thyroid, Hashimoto’s thyroiditis, and infections in the small intestines.
Many cases of under-active or “low” thyroid are due to autoimmunity or Hashimoto’s.
Autoimmunity means the immune system is on overdrive.
For some reason, the immune system “ramped” up way, starts to “attack” various tissues. In the case of Hashimoto’s, the immune system is attacking thyroid tissue. When this happens, thyroid signals get thwarted. The patient gets ill.
What does the gut have to do with this?
This study demonstrated that folks with hypothyroidism show significantly higher levels of small intestinal bacterial overgrowth (SIBO) and key bacterial distinctions than those without this thyroid condition.
This supports the idea that improving gut health could have far-reaching effects beyond digestion, possibly even helping to prevent and treat a wide variety of autoimmune diseases.
A study on Hashimoto thyroiditis and gut biome health was presented at ENDO 2025: The Endocrine Society Annual Meeting.
These findings open the door to new screening and prevention strategies,” say the authors.
Functional doctors have been saying this for years.
And getting laughed at.
Patients got laughed at.
No more!
Doctors should now begin to monitor thyroid health more closely in patients with SIBO, and vice versa.
In this study they evaluated data on 49 patients with Hashimoto thyroiditis (HT) and 323 controls without the condition from their REIMAGINE trial, which included small bowel fluid samples from upper endoscopies and DNA sequencing.
In the study, all patients with HT were treated with thyroid replacement (levothyroxine), hence, there were notably no significant differences between the two groups in terms of thyroid stimulating hormone (TSH) levels.
Despite the lack of those differences, patients with HT had a prevalence of SIBO more than “twice” that of the control group.
Independent of gender.
When the two groups were further subdivided into two groups each — those with and without SIBO.
The small bowel microbiome was not only different in SIBO-positive patients, including higher gram negatives, but the presence or absence of hypothyroidism itself was associated with specific patterns of gram-negative bacteria.
In hypothyroid patients without SIBO, there were also changes between groups, such as higher Neisseria in the hypothyroid group.
The small bowel is the most metabolically active area of the intestine.
Changes here can have far reaching changes in your health.
The small bowel is where we digest nutrients. Where we get “fed” from food.
When you think of digestion, getting your “umph” from food, the small bowel is center stage.
The small bowel breaks down carbohydrates, proteins, and fats into smaller molecules (sugars, amino acids, fatty acids) that can be absorbed into the bloodstream.
If there are infections (bad bugs) inside the small intestine, which ideally should be much more sterile that the diverse biome in the large intestine, these “bugs” compete with us for our food.
We then eat.
But our cells starve.
- If you have any autoimmune disease, it makes sense to work with a well trained functional provider.
- To do a deep dive into your gut.
In a separate analysis, this same team evaluated data from the TriNetX database on the 10-year incidence of developing SIBO among 1.1 million subjects with hypothyroidism in the US compared with 1 million controls.
They found that people with hypothyroidism were approximately “twice” as likely to develop SIBO compared with those without hypothyroidism.
- Treatment of under-active thyroid had gut benefits.
- It decreased the risk of developing SIBO in hypothyroidism vs. those who did not receive treatment.
How does SIBO influence the gut?
- SIBO leads to inflammation.
- SIBO leads to a weakening of the gut barrier.
- When the gut wall “opens”, with SIBO, is has trouble “closing” again.
Thyroid replacement absorption and cycling of the thyroid hormone occurs predominantly in the small bowel, [while the] microbiome plays a key role in the absorption of iron, selenium, iodine, and zinc, which are critical for thyroid function.
- A propensity to SIBO may come from an adversely altered microbiome changes secondary to reduced thyroid hormone signaling!
Got autoimmune issues? Such as: Hashimoto’s, Type 1 Diabetes, MS, RA, mixed mucosal disease, and on and on?
Get a doc that respects the role of your gut in your vulnerability to these issues, and then has been trained to track, treat and reverse these gut issues.
To put your autoimmunity in your rear view mirror.
Knowledge is power.
Learn More at Our Las Vegas Office
Learn More at Our Las Vegas Office
If you’ve been feeling unheard or stuck with symptoms that don’t seem to add up, there’s a good chance your gut might be playing a bigger role than you realize. At Synergetics Health and Wellness, Michelle Johnson takes a whole-person approach to thyroid and digestive health—looking beyond labels to understand what your body is really trying to say. If you’re in the Las Vegas area, we’d love to help you get the answers and support you deserve. Call 702‑240‑3533 or reach out through our contact form to get started.
