Relationship Between SIBO and Hashimoto’s

Relationship Between SIBO and Hashimoto’s

Hashimoto’s and SIBO are often seen together and it's not always clear which one comes first. The truth is SIBO can be a cause or contributing factor to Hashimoto's but Hashimoto's or hypothyroidism can also lead to or exacerbate SIBO.

Many disorders cause changes in gastrointestinal (GI) motility. Reduced motility is one of the risk factors for small intestine bacterial overgrowth (SIBO).  Changes in GI motility are often seen in those with hypothyroidism.

These changes can cause a shift in the bacterial equilibrium in the small intestine, which could lead to bacterial overgrowth. The correlation between hypothyroidism or Hashimoto's and SIBO is discussed in this post.

I’ll also share my personal experience with Hashimoto's and SIBO thus far. Check it out below. 

**Just a quick heads up- this post contains affiliate links which means if you click on them and buy something,  I will earn a small commission (at no additional cost to you) to help continue maintaining this site.

Note to readers: This site does not provide medical advice. It is intended for informational purposes only. It is not a substitute for professional medical advice, diagnosis or treatment. Consult your doctor before making any medical decisions.  

sibo and hashimoto's hypothyroidism

What is SIBO?

Small intestinal bacterial overgrowth (SIBO) occurs when the overall bacterial population in the small intestine increases abnormally. SIBO is usually caused by a condition — such as surgery or sickness — that inhibits the passage of food and waste materials through the digestive tract, allowing bacteria to proliferate.

When the small intestine is overloaded with bacteria, especially the wrong kind, it can cause unpleasant symptoms like gas and diarrhea. It can also reduce your ability to digest and absorb nutrients from food. 

Small intestinal bacteria break down carbs and convert them to gas and short-chain fatty acids. More bacteria can lead to more gas and other waste products, which can lead to diarrhea.

The bacteria also eat proteins and vitamin B12 (which are meant for us, not the bacteria), as well as bile salts that are supposed to aid fat digestion. All of this leads to poor fat digestion and absorption, especially when it comes to calcium and fat-soluble vitamins.

What are the Symptoms of SIBO?

SIBO symptoms are similar to those of a range of other GI disorders and is being researched as a possible cause of IBS. SIBO symptoms differ from person to person, depending on how serious the bacterial overgrowth is and whether the person has any coexisting conditions.

Symptoms may include:

  •       bloating
  •       diarrhea
  •       constipation
  •       vitamin deficiencies, especially A, D, K, and  B12

The symptoms may also be determined by the type of bacteria that is taking over the GI tract. Research has shown that hydrogen-producing bacteria are linked to diarrhea, while methane-producing bacteria are linked to constipation.

Types of SIBO

SIBO is classified into two types based on the primary forms of gas produced by the bacterial overgrowth in the small intestine. SIBO exists in different forms, each with its own set of issues and complications.

  • Hydrogen Dominant (SIBO-D)

If you have SIBO with diarrhea (SIBO-D), your small intestine is most likely overrun with hydrogen-producing bacteria. As a consequence of carbohydrate fermentation in the digestive system, bacteria produce hydrogen gas.

This is a perfectly normal process and hydrogen is produced as a byproduct of fermentation in our large intestine. We start to have a problem when large amounts of hydrogen gas are produced in the small intestine. Excess hydrogen can result in a quick transit time and/or loose stools.

  •       Methane Dominant (SIBO-C)

Our intestinal flora also includes archaea, which are bacteria-like organisms. Archaea are single-celled organisms without a nucleus, which distinguishes them from bacteria.

Archaea in our intestines feed on hydrogen produced by bacteria during the fermentation of carbohydrates. As a result of their digestion, Archaea produce methane. The more fiber and hydrogen gas fermentation that happens in the intestines, the more methane the archaea produces.

An overpopulation of archaea in the gut has been linked to lactose malabsorption and impaired digestive tract motility. Constipation and bloating are other possible side effects.

sibo and hashimoto's

What is the Connection Between SIBO and Hashimoto’s

SIBO is a common complication of hypothyroidism. Conversely, it can also contribute to the development of Hashimoto's.

The occurrence of SIBO has been found to be as high as 50 percent in people with hypothyroidism. SIBO occurs when the number of bacteria in your small intestine increases or the types of bacteria present change.

By influencing the enteric nervous system and the migrating motor complex (MMC), thyroid hormones play an important role in gut motility. Between meals, the migrating motor complex (MMC) sweeps across the colon to keep food moving through the digestive tract. 

Thyroid hormones affect the rate at which food is digested and passes through your intestines. This entire process slows down when you have Hashimoto's and your thyroid hormone levels are low. This is why constipation is one of the defining symptoms of Hashimoto's.

All of the food lodged in your small intestine feeds the bacteria there, increasing the bacterial overgrowth. By eliminating SIBO and healing your gut, you can reduce your immune system's attack on your thyroid and reduce your Hashimoto's symptoms.

Reactive foods should be avoided and nutrient depletions should be replenished with restorative meals and supplements. In many cases, supporting the gut with probiotics is also helpful for people with Hashimoto's.

Other Conditions Linked to SIBO

Beyond autoimmune thyroid disease, SIBO is being linked to a bunch of other conditions as well such as:

  • Acid Reflux 13
  • Celiac Disease
  • IBS
  • Skin Issues- Have you heard of the gut-skin axis? It's a thing. Basically it just means that what happens in the gut can effect the skin.
  • Endometriosis 12
  • Depression and Anxiety 15
  • GI Cancers 14

What Causes SIBO?

SIBO is a medical disorder in which bacteria in the intestines grow out of control. This does not usually happen in those who are in good health. Certain factors have been linked to an increased probability of this happening. A few of these include:

  •       Low Motility

Normally, the intestines push food and bacteria through the digestive tract, preventing an excessive buildup of bacteria in the small intestine. This mechanism slows down if someone has low motility, causing food to ferment in the small intestine.

  • Low Levels of Stomach Acid

Since stomach acid inhibits bacterial growth, there are few or no bacteria in the stomach, and the number is low even in the upper small intestine. Hypochlorhydria (low stomach acid) is, therefore, a risk factor for SIBO.     4 Taking antacids and proton pump inhibitors for reflux can raise the risk for hypochlorhydria. 

  • Chronic Pancreatic Disease

Chronic pancreatitis is another cause of SIBO, as it lowers small intestine motility due to local inflammation. It also necessitates the use of powerful narcotics, which slow the gut even more. SIBO is more likely in this situation because of the increased risk for intestinal blockage.  4

  • Diabetes

GI motility issues can occur in people with uncontrolled diabetes or persistent hyperglycemia because high blood sugar levels can slow GI transit time. 9 Studies have found SIBO occurrence to be as high as 53% in diabetics. 7 In particular, research has suggested that SIBO is even more common in diabetics that have peripheral neuropathy. 8

  • Celiac disease

SIBO can develop as a result of celiac disease disrupting intestinal motility. Two-thirds of patients with overgrowth responded to treatment with a reduction in symptoms, according to one study, especially when they did not respond to gluten-free diets.

  • Alcoholism 11

Things That Protect Against SIBO

  • Motility/Migrating Motor Complex (MMC)- the MMC keeps undigested food moving along through the small intestine.
  • Adequate Stomach Acid
  • Pancreatic Enzymes/Proper pancreatic function

How to Test for SIBO

There are various tests out there for bacterial overgrowth, inadequate fat absorption, and other abnormalities that may be contributing to your symptoms. The following are some examples of common tests used to test for SIBO:

  •     Small Intestine Aspirate and Fluid Culture

This is the gold standard test for bacterial overgrowth. A long, flexible tube (endoscope) is sent down the throat and across the upper digestive tract to the small intestine to obtain the fluid sample. A sample of intestinal fluid is taken and tested in a lab for bacterial growth.

  •  Breath Testing

This is a much less invasive test and more commonly used. It determines how much hydrogen or methane you breathe out after consuming a glucose or lactulose and water mix. Exhaled hydrogen or methane levels that rise quickly could signify bacteria growth in your small intestine. The lactulose breath test is the most common test currently used to diagnose sibo. 10 This is the kind of test I used to diagnose my SIBO.

sibo breath test

How to Get Rid of SIBO

         The most common treatment for SIBO is antibiotics. However, research suggests that dietary adjustments, such as restricting sugar and lactose, can help to prevent bacterial overgrowth. Antibiotics and probiotics can be used in conjunction with the SIBO diet.

Drinking plenty of water can also help with discomfort and digestion. Discuss the risks with your doctor or dietitian before making any dietary changes or starting any new treatment.

  •       Herbal Supplements

If you don't want to take antibiotics, herbal antimicrobials are an option. One study found that herbal therapies are at least as effective as antibiotic therapy.

One of the most common supplements for treating SIBO naturally is enteric-coated peppermint oil. The treatment normally lasts one to six months. One to two capsules of enteric-coated peppermint oil three times a day is a normal dose. It should be taken with a glass of water in between meals.

  •      SIBO Diets

During treatment, alternative medicine professionals will normally advise you to follow a diet that restricts your intake of sugary and starchy foods.

The specific carbohydrate diet (SCD) is one such diet. Grains, starchy vegetables, and several legumes are avoided in this diet.

Other diets include the low FODMAP diet and low fermentation diet.

Then there's the elemental diet which is basically a liquid diet- a specially formulated powdered drink that is meant to starve the SIBO bacteria. It contains amino acids, partially hydrolyzed carbohydrates, medium-chain triglycerides, vitamins/minerals- basically, everything one needs to survive for up to 4 weeks or so. 

I ended up using this method as recommended by my functional medicine practitioner for my SIBO. It did get rid of it. I was on it for 2 weeks and used about 4 of the larger bags. I drank a little black coffee along the way but otherwise, just the elemental shakes.

It actually wasn’t too bad and I didn’t have many cravings. Easing back into eating regular foods again and getting regular digestion back on track did take a little time though. 

The shakes are unfortunately quite pricey but supposedly have a higher success rate at getting rid of the SIBO when compared with other methods. I’ve heard of some people trying to make their own elemental formulas but that they don’t generally taste very good at all. 

elemental diet for sibo

My experience with SIBO and Hashimoto’s

I’ve been working with a functional medicine practitioner for about a year to try to figure out underlying causes for my Hashimoto’s. I’ve done a ton of tests during this time from stool tests, to heavy metal testing to hormone testing, etc. The SIBO test was almost done on a whim..I didn’t have super obvious GI symptoms, so I did not think it would be positive. However, out of all the tests I’ve done, the SIBO test was the main one that popped.

 As mentioned above, I ended up doing the elemental formula for 2 weeks and then retested to be sure it was gone. My digestion has gotten much better since treating the SIBO. That being said, I’m still on the hunt for other underlying causes because I still have random Hashimoto's symptoms that I can’t explain. 

SIBO Recurrence Rates

         SIBO has a high recurrence rate, with up to a 40% recurrence rate even after effective treatment. However, there are techniques to manage SIBO symptoms and restrict bacterial growth through diet.

How to Prevent SIBO Recurrence?

         If you do not make permanent adjustments to your diet or lifestyle, SIBO may reoccur.

SIBO prevention tips include:

  •       Sugar and processed carbs should be avoided.
  •       If probiotics make your symptoms worse, stop taking them.
  •       Reduce your everyday stress levels
  •       Exercise regularly
  •       Because gut motility is usually the cause of overgrowth in your small intestine, ensuring that it is restored is crucial to preventing a SIBO relapse.
  •       If a medical condition is the fundamental cause of your SIBO, treating that illness may help you get rid of it for good.

Conclusion:  SIBO is most commonly caused by an underlying condition. Work with a doctor to build a long-term treatment plan if you have a chronic ailment like Crohn's disease or celiac disease. SIBO is curable, but it may reoccur. If left untreated, it can lead to dehydration and malnutrition. If you feel you have SIBO, see your doctor as soon as possible so you can begin treatment.

Don’t forget to follow me on Instagram @foodcourage for the latest AIP/Paleo recipes, autoimmune nutrition info, and Food Courage happenings!


  1. Quigley, E. M. (2019). The spectrum of small intestinal bacterial overgrowth (SIBO). Current gastroenterology reports, 21(1), 3
  2. Sachdeva, S., Rawat, A. K., Reddy, R. S., & Puri, A. S. (2011). Small intestinal bacterial overgrowth (SIBO) in irritable bowel syndrome: frequency and predictors. Journal of gastroenterology and hepatology, 26, 135-138.
  3. Chedid, V., Dhalla, S., Clarke, J. O., Roland, B. C., Dunbar, K. B., Koh, J., ... & Mullin, G. E. (2014). Herbal therapy is equivalent to rifaximin for the treatment of small intestinal bacterial overgrowth. Global Advances in Health and Medicine, 3(3), 16-24.
  4. Shah, S. C., Day, L. W., Somsouk, M., & Sewell, J. L. (2013). Meta‐analysis: antibiotic therapy for small intestinal bacterial overgrowth. Alimentary pharmacology & therapeutics, 38(8), 925-934.
  5. Miazga, A., Osiński, M., Cichy, W., & Żaba, R. (2015). Current views on the etiopathogenesis, clinical manifestation, diagnostics, treatment, and correlation with other nosological entities of SIBO. Advances in medical sciences, 60(1), 118-124.
  6. Jaime P. Almandoz, Hossein Gharib, Hypothyroidism: Etiology, Diagnosis, and Management, Medical Clinics of North America, Volume 96, Issue 2, 2012, Pages 203-221, ISSN 0025-7125,
  7. Yan LH, Mu B, Pan D, et al. Association between small intestinal bacterial overgrowth and beta-cell function of type 2 diabetes. J Int Med Res. 2020;48(7):300060520937866. doi:10.1177/0300060520937866
  8. Rana SV, Malik A, Bhadada SK, Sachdeva N, Morya RK, Sharma G. Malabsorption, Orocecal Transit Time and Small Intestinal Bacterial Overgrowth in Type 2 Diabetic Patients: A Connection. Indian J Clin Biochem. 2017;32(1):84-89. doi:10.1007/s12291-016-0569-6
  9. E. S. Björnsson, V. Urbanavicius, B. Eliasson, S. Attvall, U. Smith & H. Abrahamsson (1994) Effects of Hyperglycemia on Interdigestive Gastrointestinal Motility in Humans, Scandinavian Journal of Gastroenterology, 29:12, 1096-1104, DOI: 10.3109/00365529409094894
  10. Chedid V, Dhalla S, Clarke JO, et al. Herbal therapy is equivalent to rifaximin for the treatment of small intestinal bacterial overgrowthGlob Adv Health Med. 2014;3(3):16-24. doi:10.7453/gahmj.2014.019
  11. Gabbard SL, Lacy BE, Levine GM, Crowell MD. The impact of alcohol consumption and cholecystectomy on small intestinal bacterial overgrowth. Dig Dis Sci. 2014 Mar;59(3):638-44. doi: 10.1007/s10620-013-2960-y. Epub 2013 Dec 10. PMID: 24323179.
  12. Moore JS, Gibson PR, Perry RE, Burgell RE. Endometriosis in patients with irritable bowel syndrome: Specific symptomatic and demographic profile, and response to the low FODMAP diet. Aust N Z J Obstet Gynaecol. 2017 Apr;57(2):201-205. doi: 10.1111/ajo.12594. Epub 2017 Mar 17. PMID: 28303579.
  13. Kim KM, Kim BT, Lee DJ, Park SB, Joo NS, Kim YS, Kim KN. Erosive esophagitis may be related to small intestinal bacterial overgrowth. Scand J Gastroenterol. 2012 May;47(5):493-8. doi: 10.3109/00365521.2012.668932. Epub 2012 Mar 15. PMID: 22416969.
  14. Ma X, Wang H, Zhang P, Xu L, Tian Z. Association between small intestinal bacterial overgrowth and toll-like receptor 4 in patients with pancreatic carcinoma and cholangiocarcinomaTurk J Gastroenterol. 2019;30(2):177-183. doi:10.5152/tjg.2018.17512
  15. Banerjee A, Sarkhel S, Sarkar R, Dhali GK. Anxiety and Depression in Irritable Bowel SyndromeIndian J Psychol Med. 2017;39(6):741-745. doi:10.4103/IJPSYM.IJPSYM_46_17

Leave a Reply

Your email address will not be published.