Hypothyroidism Linked to Small Intestinal Bacterial Overgrowth (SIBO)

Small intestinal bacterial overgrowth & the stomach acid connection.

If you have hypothyroidism, your gut could play a role in your symptoms. Namely, small intestinal bacterial overgrowth (SIBO) may be present too. About 30% of people who have hypothyroidism have low stomach acid, according to high-quality research. Low stomach acid can increase your risk of small intestinal bacterial overgrowth (SIBO). The science also shows a direct link between SIBO and hypothyroidism. When trying to improve how you feel, consider healing your gut with probiotics and possibly supplemental hydrochloric acid. Learn more about what to do in this video.

Dr. Michael Ruscio, DC: Hi, this is Dr. Ruscio, and being hypothyroid has been associated with increased risk of small intestinal bacterial overgrowth through the causative mechanism of low stomach acid production. But there’s good news, this causative mess that can frustrate patients because they can’t figure out where their symptoms are coming from actually has a solution. And if you understand this domino rally of causative events that can cascade, it’s actually not too difficult to clean up the mess. But there’s one important factor that must be included in how we look at a patient with hypothyroidism, especially one who is still suffering from and describing symptoms and that is the gut connection.

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Dr. R’s Fast Facts Summary

How to know if you should use stomach acid?

  • History of anemia
  • Autoimmune condition
  • Chronic use of painkillers for example NSAIDs
  • Age: over 65

What to do?

  • Address SIBO (FIRST)
  • Perform trial on supplemental acid (HCl)
    • Experiment, do you feel better after taking HCl?
    • If you react to acid (heartburn/warmness), stop taking it

What does the research say?

Hypothyroid increases risk of low stomach acid

  • Roughly 30% association hypothyroid to low stomach acid (estimates vary) 1

Low stomach acid increases the risk of SIBO

  • Proton pump inhibitors moderately increase the risk of small intestinal bacterial overgrowth 2
  • Effects of proton pump inhibitors on the small intestine 3
  • Gut dysbiosis associated with the use of proton-pump inhibitors (PPIs) has been found to lead to the occurrence of infectious and inflammatory adverse events 4
  • Podcast with Dr. Richard McCallum suggests SIBO might be from low stomach acid allowing oral bacteria to overgrow

Hypothyroid have increased risk of SIBO

Probiotics are powerful for SIBO – See our 3 probiotics

  • Probiotics for Preventing and Treating Small Intestinal Bacterial Overgrowth: A Meta-Analysis and Systematic Review of Current Evidence 6

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Here’s the simple causal cascade I’d like to layout for you. We’ll include all of the supporting references in a moment. One thing I am always very careful to do when we are discussing hypothyroidism is to use high-quality references.  I have been appalled with the amount of fictitious and erroneous claims that are made on the internet regarding hypothyroidism.  It’s very disheartening to see the reinforcement of this quest for the thyroid to be the cause of patient symptoms in the published literature when there may be another layer, the gut, that is completely overlooked.

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When that layer is finally addressed, symptoms improve. While the thyroid may be involved, oftentimes adequate care and attention to the thyroid has already been given.  However, this other causative issue, the gut, which is causing these symptoms, including things like fatigue and brain fog and constipation has been unaddressed, and this needs to be included in a care plan to make sure that you’re seeing the optimal improvements in your health.

The SIBO Flowchart

Here’s the flowchart. Hypothyroidism increases the risk of low stomach acid. There have been a number of studies that show this averaging out at a finding of about 30%.   30% of those with hypothyroidism appear to have low stomach acid, and there’s enough data there to consider this a non-refutable statement. Second, low stomach acid increases the risk of SIBO. There have also been a number of reports that have documented this.

Now, we can’t say because hypothyroidism leads to low stomach acid and low stomach acid is associated with SIBO, that there is a definite connection between hypothyroid and SIBO, however, there is an inference. Thankfully we have data connecting this circle showing that

those who have hypothyroidism actually do have an increased prevalence of small intestinal bacterial overgrowth. We’ve discussed in the past a study in over 1800 patients that looked at a number of factors associated with being hypothyroid.  The chief factor in this study was actually small intestinal bacterial overgrowth which shocked researchers. So every point in this causal domino rally, if you will, does have evidence to support it.

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The next question we should be asking is: What can we do about it? First, we want to address SIBO or small intestinal bacterial overgrowth.  In my experience, going to a doctor and being tested is not where you want to start.  Why? Because we have 5 clinical trials to date which have been summarized in a meta-analysis showing that probiotics can clean small intestinal bacterial overgrowth of the small intestine. You don’t need to see a doctor in order to use a probiotic.  Of course, there is a time and a place for seeing a doctor and if you have specific concerns, you should go see a doctor.

But let’s say you’re hypothyroid, and you’re not feeling great and your doctor has told you that your thyroid levels are normal.  In this case, you may want to go on a probiotic protocol for a few months and then reassess because if you do have a small intestinal bacterial overgrowth, there’s a strong chance based upon the data that a good probiotic protocol will be able to decontaminate the small bowel of small intestinal bacterial overgrowth.

That’s a good starting point, and it doesn’t really matter if you do or don’t have SIBO, you can still go on a probiotic protocol. It is absolutely fine to run a probiotic protocol if you do not have SIBO. You can start there and really you can go through a good probiotic protocol at the same cost for a doctor’s office visit. Again, if you have concerns, always check in with your doctor, keep your doctor in the loop. But this may be a way to mitigate unnecessary office visits.

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So first, we try to rebalance what’s going on in the gut. That’s the probiotic protocol. Then second, you can try a supplemental hydrochloric acid to see if you notice any further symptomatic improvement. The reason why I recommend doing this after the probiotic protocol is so that you don’t have the confounding symptoms that can come from the SIBO. First, we try to clean out the small intestinal bacterial overgrowth. You’ll likely say, “Okay, I’m feeling better.” Then you can try the supplemental acid, betaine hydrochloride or betaine HCL and see if your symptoms improve even more. Perhaps your digestion feels better, you feel less bloated, you feel like you digest your food better.

Alternatively, you may notice that when taking hydrochloric acid as a supplement, you experience some reflux or a warmness or a burning sensation and that will tell you that you don’t need to supplement with digestive acid.  There are also a few factors that you can look at in your own history that will tell you if you an increased probability of being low in stomach acid, which will inform whether you need to supplement with this or not.

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The factors I’ve put up here on the screen would tell you if you’re at an increased risk for low stomach acid,  requiring supplementation. These factors include a history of anemia if you have an autoimmune condition. Of course, if you have been diagnosed with Hashimoto’s, the main underlying cause of hypothyroidism or any other type of autoimmune condition, this increases your probability. If you have chronic use of painkillers or NSAIDs and/or if you are over the age of 65. All of these can lead to a 50% prevalence of low stomach acid.  50%, that’s one in two, not everyone.

The One-Two Approach

Just because this association exists doesn’t mean that you should blindly use supplemental stomach acid unless you have some subjective sense that you feel better when using it. This is the reason for my one-two approach.  1.) Start with the probiotic protocol, attempt to get the gut as balanced as possible.   This provides a consistent baseline for the second step, Hydrochloric acid supplementation.  Evaluate any improvement or regression in how you feel. The improvements indicate the need to continue with the supplement, the regressions and even negative reactions like that warm burning sensation indicates that you should not use the acid.

This is a great way to get started. We will put all the references in the transcript associated with this post and I would encourage you if you’re at all skeptical to look at those as I try to be very cautious in the statements that I make. Everything that we’ve covered here is supported by a good level of evidence.  This is important for the hypothyroid patient who is suffering from symptoms.  Consider doing some work to improve your gut health before going further down the road of trying to optimize your thyroid hormone levels. This is the real proverbial fork in the road that I think needs to be changed in care today.

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It seems that many patients are being pushed to run these elaborate thyroid assays and try to tweak and change their medication prematurely instead of cleaning up a problem in the gut first. There’s a time and a place for both.  If you want to have the most logical sequence of interventions, first start on a thyroid hormone medication and attempt to get your thyroid hormone levels in the normal lab range, not the functional medicine ranges that are very, very narrow, but in the normal lab ranges. This gets you in the ballpark. If you’re not feeling well there, then do some work to improve your gut health.   If your symptoms clear, it tells you that those symptoms were coming from the inflammation and other imbalances in your gut, not because hormones needed to be fine-tuned.   However, if after taking steps to improve your gut health, you’re not feeling better, then move to try to fine-tune the levels of your thyroid hormone medication.

Taking the Cautious Route

Of course, keep your doctor in the loop, but at the same time be cautious.  Often patients are taken down what I find to be an unfruitful road of attempting to dial in thyroid hormone levels, doing a free T3, reverse T3, considering adding in with let’s say levothyroxine cytomel or just going from Synthroid to a combination therapy like Armour.

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It’s important to be aware of this and really understand that because I’ve seen a number of patients in the clinic that have gone down that road and not really gotten anywhere. And we’ve actually published three case studies in our clinicians’ newsletter in the past two months documenting this. When they finally took some steps to improve their gut health, all of the symptoms they thought were being driven by their thyroid went away. So I share this, in an attempt to prevent a thyroid patient from going down an unfruitful road.

Again, there is a time and a place for both of these interventions for optimizing or trying to fine tailor your thyroid hormone medication and for optimizing your gut health. I would put the optimization of gut health first and then consider the fine-tuning. Often fine-tuning isn’t necessary once you’ve improved the health of your gut.   There is a cascade.

Episode Wrap-Up

When you’re hypothyroid, you have at least a 30% chance of lower stomach acid, and that lower stomach acid has been shown to increase the prevalence of SIBO.

Now there is good news that SIBO can be simply and safely, without the need for testing, rectified by the use of probiotics.   It can be used as a preventative guard to decrease the probability that SIBO will return.  Stomach acid can be used to improve your digestion, prevent anemia, and help to supplement with what your stomach may not be making enough of, which is your stomach acid. If you’re hypothyroid and floundering with what to do, hopefully, this helps to dispel some confusion and give you a few actionables to try to get to the root cause of where symptoms are coming from and how to address them.

What do you think? I would like to hear your thoughts or experience with this.


I care about answering your questions and sharing my knowledge with you. Leave a comment or connect with me on social media asking any health question you may have and I just might incorporate it into our next listener questions podcast episode just for you!

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