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The Hypothyroidism-SIBO connection

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Do you see a lot of patients with small intestinal bacterial overgrowth? While the underlying causes of SIBO are diverse, one that has received more attention in the literature lately is low thyroid function. Read on to learn how hypothyroidism can impair gut motility and contribute to the pathophysiology of SIBO.

A healthy small intestine contains relatively few microbes. Antimicrobial peptides, the acidity of incoming chyme from the stomach, and gastrointestinal motility all help maintain this relatively low bacterial load (1). However, if these systems break down, small intestinal bacterial overgrowth (SIBO) can develop.

I’ve written extensively about the pathophysiology of SIBO and why it’s so difficult to treat. Treatment not only involves addressing the overgrowth with antibiotics or herbal antimicrobials, but also restoring the mechanisms that prevent overgrowth from recurring. This includes proper thyroid function. In this article, I’ll discuss why thyroid function impairs gut motility, the association between hypothyroidism and SIBO, and why thyroid panels are a must in patients with SIBO and irritable bowel syndrome (IBS).

Meet the Migrating Motor Complex

The gut has a dense, mesh-like network of more than 500 million neurons that, along with other nerve cells, form the enteric nervous system (ENS). The ENS innervates the smooth muscle cells that line the intestine and governs intestinal mixing and peristaltic contractions.

Thyroid function impairs gut motility, so if you’re suffering from IBS or SIBO, a thyroid panel is a must

During times of fasting, the ENS sends waves of electrical activity through the small intestine, moving the contents along the gastrointestinal tract to the colon. This is called the migrating motor complex (MMC). The MMC is crucial for keeping bacteria out of the small intestine and in the colon, where they belong. In animal models, drugs that disrupt MMC function have been shown to cause SIBO, while restoring MMC function reduces the density of small intestinal bacteria to normal levels (2, 3).

The MMC is affected by numerous conditions, including anatomical abnormalities such as gastrointestinal surgery, intestinal diverticula or fistulas, and diseases of neuropathic, autoimmune, inflammatory, or metabolic nature (4). It’s also influenced by endocrine disease, including thyroid function. In the next section, I’ll discuss how poor thyroid function can impair MMC function and motility.

The Thyroid and Motility

Thyroid hormones influence gut motility by modulating the ENS and altering smooth muscle function and the MMC (5, 6). Studies in both animals and humans have shown that hypothyroidism is associated with delayed gastric emptying, decreased frequency of intestinal peristalsis, and slower orocecal transit time (7, 8). This slower transit time from the oral cavity to the end of the small intestine often results in constipation, which is the most frequent gastrointestinal complaint in patients with hypothyroidism (9).

However, some patients may have slow orocecal transit time followed by rapid colonic transit time, resulting in diarrhea. This is thought to be due to carbohydrate malabsorption and fermentation in the distal ileum, which then leads to high osmolality in the colon. A study published in January 2017 found that 29 percent of patients with IBS had delayed orocecal transit time, but there was no difference in the presence of delayed transit between subtypes (diarrhea, mixed, or constipation) (10).

The Association between Hypothyroidism and SIBO

Now that we understand why thyroid would impact gut motility, let’s look at a few studies that have assessed hypothyroidism and SIBO in humans:

Study 1: A group of researchers in Italy wanted to determine whether a history of overt hypothyroidism due to autoimmune thyroiditis was associated with SIBO. They recruited 50 patients with hypothyroidism and 40 healthy controls (11). Patients with hypothyroidism were given synthetic T4 and achieved normal thyroid levels prior to performing glucose breath tests (GBT). Astoundingly, they found that 27 out of the 50 patients with a history of hypothyroidism (54 percent) were positive for SIBO, compared to 5 percent of controls (two of 40).

They further found that abdominal discomfort, flatulence, and bloating were all common in the hypothyroid patients with SIBO, but there was no significant correlation between hypothyroidism and bowel frequency (constipation or diarrhea). After a one-week course of rifaximin, 19 of the 27 patients (70.4 percent) were negative for SIBO according to a repeat glucose breath test and had significantly improved self-reported abdominal discomfort, flatulence, and bloating.

Overall, this study identifies prior hypothyroidism as a risk factor for SIBO, suggesting that once SIBO develops in a hypothyroid state, restoring normal thyroid status may not be enough to clear bacterial overgrowth. It’s unfortunate that no breath tests were performed before thyroid medication was begun—it would have been interesting to see if any patients successfully eradicated their SIBO simply from restoring thyroid hormone levels. We’ll have to hold out for future studies!

Study 2: In this study, researchers in Poland recruited 34 patients with diarrhea-predominant SIBO (SIBO-D), 30 patients with constipation-predominant SIBO (SIBO-C), and 30 healthy controls. Thyroid hormone levels were similar in controls and patients with SIBO-D, but patients with SIBO-C often had thyroid panels that were characteristic of hypothyroidism. Both SIBO groups had elevated anti-thyroid peroxidase (ATPO), with SIBO-C patients having the highest levels (12).

Study 3: Researchers in Germany performed a retrospective cohort study of 1,809 patients to assess various risk factors for SIBO. They found that hypothyroidism and T4 therapy were associated with a 2.6 and 3.0 times increased risk of SIBO, respectively (13). While the authors suggested that T4 medication itself might somehow be contributing to SIBO, I think it’s more likely that those on T4 therapy had more severe hypothyroidism in the first place, which required more aggressive intervention.

Treating SIBO in Cases of Hypothyroidism

There’s certainly still a lot we don’t know, but hopefully this article helps illuminate the connection between hypothyroidism and SIBO. Here are some practical takeaways that you can put into practice in your clinic:

Perform a Full Thyroid Workup on all Patients with SIBO or IBS

All patients with SIBO or IBS should receive a full thyroid panel, including thyroid antibodies, as part of their routine lab work. Thyroid conditions are quite common, and an estimated 60 percent of people with thyroid disease are unaware of their condition (14). While no studies to date have been done on subclinical hypothyroidism (SH) and SIBO, I would venture to guess that SH contributes to SIBO as well, just to a lesser degree.

Support Thyroid Function with Diet and Lifestyle Changes

I’ve written several articles on how to improve thyroid function by correcting nutrient deficiencies, rebalancing the immune system, and making simple diet and lifestyle changes. In many patients, reducing inflammation and eating a nutrient-dense diet can help restore thyroid function and proper gut motility.

Consider Thyroid Medication to Support Motility

While diet and lifestyle changes will improve thyroid function over time, many patients, particularly those with constipation, will benefit from acute thyroid support to help with motility.

Consider other Motility Enhancers

If thyroid support does not restore normal bowel function in patients with constipation, motility enhancers like low-dose naltrexone (LDN), low-dose  erythromycin, Iberogast, 5-HTP, or MotilPro can also be considered. Motility enhancers have been shown to delay the recurrence of SIBO (15).

Treat the Overgrowth

While slow transit is often what allows SIBO to occur in the first place, speeding up transit will not necessarily be enough to clear the overgrowth once the microbes have set up camp. However, it’s important to remember that treating the overgrowth will only be successful in the long term if we simultaneously address the underlying cause of low motility.


  1. Chris…..How about beriberi as a cause for sibo? Not old school alcoholic or malnutrition berineri…but modern day SAD, high calorie- high carbohydrate malnutrition. All the sugar messing up the brains ability to use thiamine. Which then causes body wide neuropathies, especially autonomic neuropathy, which leads to gut motility problems and sibo. Your thoughts…… thanks, mike

  2. I just realized what my problem was – SIBO – through a blog I was reading one day. I’ve been to dr after dr and they couldn’t figure it out. I found a dr they mentioned on the blog (otherwise I had no idea where to start looking) and he said I had SIBO, but he didn’t say anything about the methane/hydrogen oriented SIBO. Is there a test I can purchase to see which I have? Or do I have to see a dr to get that test performed? He prescribed Xifarin, but he didn’t do a breath test. I think he didn’t know there was a difference. Thanks for your help.

    • Yes! Contact me and I can order you one and work with you on SIBO. I trained with the Kresser Institiute last year. I’d be happy to guide you!

      • If I give you my SIBO info can you also help me? And what do you charge? Thank you.

  3. Hi Chris,
    You state “A healthy small intestine contains relatively few microbes.” yet I was under the assumption we have or should have something like 1-1/2 to 2 quadrillion bacteria in our small intestine…this is hardly relatively few! Can you expound on this? Thank you

    • Bacteria should be abundant in the LARGE intestine, but the small intestine should be relatively sterile

    • your large intestine ( colon) is where most of the bacteria should reside not the small intestine.

    • Hi Val,
      The bacteria you mention, that we know we want and need in our guts, belong in the *large* intestine, which is further on in the digestive tract. The presence of a lot of them in the *small* intestine, which is right after the stomach, is what SIBO means; Small Intestinal Bacterial Overgrowth.

  4. Have you considered tspecial new discovery tributyrin complex that gets into the small and large intestine? Not like sodium magnesium butyrate?
    Would you like some info email me:) We like to help each other out:)

  5. Hi Chris,
    I donated a lobe of my liver to my son and that is about when the digestive trouble started. I have done a SIBO protocol with good results but I am repeating it now as symptoms have been creeping back up on me. I have suspected for a while that I have a motility problem. Do you know if motility enhancers are effective for MMC disruption caused by gastrointestinal surgery?
    Thank you for all your hard work.
    Mitya (RN and future acupuncturist)

  6. Could the same factors (slowed peristalsis, etc.) be a potential cause for someone who has recurring candida?

  7. Which are the safe foods that you can take with no fear that it would exasperate sibo?
    If you eat a food and goes down well can it make sibo worse? won’t your digestive system repels it and makes you taste it bad or have immediate reaction if it is no good for you?
    Does sibo cause you to have night time acid reflux?
    Can you regain your lost weight if you have sibo?
    How to find the underlying cause of sibo?
    What percentage accurate is the Lactulose breath test if it is not 100% ?

  8. Chris
    Couple questions.
    1. Can you take iberogast or motilpro with atrantil together whether on full or maintainence dosage of Atrantil?
    2. Which motility med do you recommend? Iberogast or moltipro?