Millions of people are now taking medications like semaglutide (Ozempic, Wegovy) or tirzepatide (Mounjaro) to manage blood sugar or lose weight. These drugs work, and for many people they’ve made a real difference. They are a very powerful crutch.
But there’s a gut problem that’s quietly showing up in some of the people taking these medications, a gut problem that most doctors aren’t warning their patients about, as I have written about previously. It’s called SIBO, small intestinal bacterial overgrowth. And if your thyroid gland isn’t working properly, your risk could even be higher.
First, What Is SIBO?
Your digestive tract is home to trillions of bacteria. The bacteria are concentrated in the colon, the large intestine. SIBO happens when these bacteria take up residence in your small intestine, where they don’t belong in large numbers.
Having bacteria in your small intestine is a real problem. They cause a lot of bloating, gas, chronic constipation, or diarrhea that leads to fatigue, brain fog, and poor nutrient absorption.
Your body has trouble absorbing key vitamins and minerals, such as B12, iron, and magnesium, as well as other nutrients it needs to function well. SIBO can be very disruptive to your life, making it hard to eat normal foods and making social interactions centered around food extremely difficult. Carbohydrate-containing foods are particularly difficult to digest, leading to a lot of bloating and pain.
Why GLP-1 Drugs Can Trigger SIBO
GLP drugs can help you control your blood sugar. One way they do this is by slowing down how quickly food moves through your gut, and that’s on purpose. It prevents the blood sugar spikes after meals. But a sluggish gut is also the perfect environment for bacteria to grow where they don’t belong.
A large 2025 study by Dr. Yan Sun and colleagues at Case Western Reserve University examined more than 216,000 patients with diabetes. Those taking GLP-1 drugs had more than twice the risk of developing SIBO compared to people on other diabetes medications. The researchers concluded that doctors should test patients for SIBO before giving them these drugs.
Now Add a Sluggish Thyroid
Your thyroid gland — a small butterfly-shaped gland in your neck — controls your metabolism. This includes how well your food moves through your gut. When your thyroid is low, your entire digestive system slows down.
The muscles that push food forward through your intestines (peristalsis) don’t work very efficiently if your thyroid function is low. That’s the same slowdown that GLP-1 drugs cause, and the research shows that hypothyroidism (low thyroid function) already significantly raises SIBO risks on its own.
In a well-known study, Dr. Elisa Lauritano and colleagues in Rome found that 54% of patients with low thyroid function had SIBO, compared to just 5% of people with normal thyroid function. Stop for just a second and think about that. More than half of people with low thyroid function had SIBO, but people with normal thyroid function hardly had it at all. So, low thyroid function is a huge risk factor for SIBO.
A 2025 study by Dr. Ming Wei and colleagues at Cedars-Sinai found similar results, with SIBO in nearly one in three hypothyroid patients versus one in six in the control group. So this is confirmed in more than one study. Low thyroid function is very much connected to SIBO.
And here’s the surprising part: You don’t have to have a serious thyroid problem for your risk to go up. A study by Dr. Biao Wang and colleagues found that women with borderline low thyroid (a condition called subclinical hypothyroidism that often goes undiagnosed and untreated) had SIBO rates of 57% versus 32% in those with normal thyroid levels. Borderline thyroid problems are far more common than people realize.
If a GLP-1 drug is already slowing your gut, and your thyroid is adding more of the same, these two things are working together in a way that could make your life very miserable very soon.
It Goes Both Ways
The interaction goes both ways. SIBO doesn’t just result from thyroid problems; it can also help cause them. Research by Dr. Sina Mehravar and colleagues at Cedars-Sinai found that people with SIBO were 2.5 times more likely to develop Hashimoto’s thyroiditis (an autoimmune thyroid condition) over the following six years. A struggling gut appears to trigger immune system dysfunction, which then attacks the thyroid.
The gut and thyroid are connected in ways that run in both directions. You can’t fully care for one while ignoring the other.
What You Can Do to Lower Your Risk of SIBO
The good news is that you can support your thyroid function naturally with food and lifestyle. You don’t usually need medications.
Selenium
Selenium is the most important nutrient here. A 2024 review of 35 clinical trials by Dr. Valentina Huwiler and colleagues at Bern University Hospital found that selenium reduced immune markers associated with thyroid damage in Hashimoto’s patients. Brazil nuts are one of the best natural sources — one or two a day is enough. Sunflower seeds and whole grains also provide selenium.
Our Hallelujah Diet Glutathione Promoter not only has N-acetylcysteine in it, but also 200 micrograms of selenium per capsule, which is very protective for your thyroid.
Iodine
Iodine matters too, since your thyroid needs it to make the hormones that regulate your metabolism. But be careful with iodine supplements if you have Hashimoto’s — too much can actually worsen the autoimmune response in some people. Getting iodine from food (like sea vegetables in moderate amounts) is safe for most people. Hallelujah Diet Nascent Iodine can be diluted to safe levels for most people as well. Check with your provider before supplementing.
Anti-Inflammatory Diet
Beyond specific nutrients, an anti-inflammatory, plant-based, whole-foods diet supports both the thyroid and the gut. Getting rid of processed foods, eating plants, and more fiber directly reduces the inflammation that drives autoimmune thyroid disease, and helps keep gut bacteria where they belong.
Two Simple Steps to Take Now
First, if you’re on a GLP-1 drug, ask your doctor to check your thyroid. A basic TSH and free T4 blood test is all that is needed. Even borderline results are worth addressing, especially when you’re already on a medication that slows your gut.
Second, if you have SIBO, make sure your thyroid is part of the conversation. The bacterial overgrowth is just a symptom of impaired gut motility. Food is not moving through fast enough, and that is what needs to be addressed. The research has clearly shown that your thyroid function is a major player in your gut function.
GLP-1 drugs are a crutch, and they are a powerful one that many people are trying out. They give people hope that life can be different.
You still have to make lifestyle and dietary changes to keep the weight off. Check out our complete guide on healthy weight loss for more ideas. You really can’t stay on the GLP-1 drugs forever. But while you’re using them, you want to make sure you support your thyroid function so that you don’t end up with SIBO. That would put you in a worse position than you started in.
At Hallelujah Diet, our mission is to equip you so that your health empowers you to accomplish the mission that God has for you. Not sure how to get started? Learn more right here.
References
Huwiler, V. V., Maissen-Abgottspon, S., Stanga, Z., Mühlebach, S., Trepp, R., Bally, L., & Bano, A. (2024). Selenium supplementation in patients with Hashimoto thyroiditis: A systematic review and meta-analysis of randomized clinical trials. Thyroid, 34(3), 295–313. https://doi.org/10.1089/thy.2023.0556
Lauritano, E. C., Bilotta, A. L., Gabrielli, M., Scarpellini, E., Lupascu, A., Laginestra, A., Novi, M., Sottili, S., Serricchio, M., Cammarota, G., Gasbarrini, G., Pontecorvi, A., & Gasbarrini, A. (2007). Association between hypothyroidism and small intestinal bacterial overgrowth. The Journal of Clinical Endocrinology & Metabolism, 92(11), 4180–4184. https://doi.org/10.1210/jc.2007-0606
Mehravar, S., Wei, M., Leite, G., Barlow, G., Rezaie, A., Naji, P., Pimentel, M., & Mathur, R. (2025). SUN-396 Small intestinal bacterial overgrowth associated with higher risk of Hashimoto’s thyroiditis. Journal of the Endocrine Society, 9. https://doi.org/10.1210/jendso/bvaf149.2405
Sun, Y., Veccia, D., Liu, B. D. X., Tse, W., Fass, R., & Song, G. (2025). Diagnostic evaluation of an increased risk of developing small intestinal bacterial overgrowth associated with glucagon-like peptide-1 (GLP-1) receptor agonists and dual GLP-1/GIP receptor agonists: A global retrospective multicenter cohort analysis. Diagnostics, 15(17), Article 2264. https://doi.org/10.3390/diagnostics15172264
Wang, B., Xu, Y., Hou, X., Li, J., Cai, Y., Hao, Y., Ouyang, Q., Wu, B., Sun, Z., Zhang, M., & Ban, Y. (2021). Small intestinal bacterial overgrowth in subclinical hypothyroidism of pregnant women. Frontiers in Endocrinology, 12, Article 604070. https://doi.org/10.3389/fendo.2021.604070
Wei, M., Mehravar, S., Leite, G., Naji, P., Barlow, G., Hosseini, A., Rashid, M., Sanchez, M., Fajardo, C., Pimentel, M., & Mathur, R. (2025). Relationship between hypothyroidism, risk of small intestinal bacterial overgrowth, and duodenal microbiome alterations. The Journal of Clinical Endocrinology & Metabolism. Advance online publication.https://doi.org/10.1210/clinem/dgaf495
