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  • Writer's pictureGavin Guard, Medical Director

A common cause of heartburn

Updated: Jan 23, 2022

Key Takeaways

  • SIBO (small intestinal bacterial overgrowth) is a common cause of heartburn and GERD (gastroesophageal reflux disase) symptoms

  • Proton pump inhibitors (PPIs) like Prilosec and Nexium are commonly used to treat reflux symptoms

  • These medications are associated with higher rates of SIBO

  • Treating SIBO can help alleviate reflux symptoms

Does this sound like you?

Do you have any of the following symptoms?

  • Burping, belching

  • Heartburn

  • Regurgitation

  • Chronic cough

  • Feeling of something stuck in your throat

  • Excessive throat clearing

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These symptoms might indicate that you have reflux or GERD (gastroesophageal reflux disease). These symptoms are often managed with medications called Proton Pump Inhibitors, or PPIs for short. Brand names like Nexium and Prilosec are classic household staples of American medicine cabinets. However, I’ve seen too many patients rely on these medications for an extended period of time.

In this article, I will review how PPIs can actually do more harm than good and how it can make the problem that causes GERD symptoms in the first place even worse.

SIBO may be a cause of your gut issues

Small Intestinal Bacterial Overgrowth, or SIBO, is a new and upcoming diagnosis that is making its way into mainstream medicine. It is characterized by symptoms such as bloating, gas, diarrhea, constipation, reflux. More so, people with SIBO can also suffer from non-gut symptoms like joint pain, low energy, and hormonal imbalances.

Clinicians in functional medicine are often much more in tune with this potential diagnosis’ impact on gut and overall health. This is because 15-20% of the overall population has SIBO. Even more surprising, SIBO is present in 65-84% of those with irritable bowel syndrome (IBS), and is a main factor causing IBS symptoms.

Learn how probiotics can help SIBO and IBS

Normally, most of your gut bacteria is localized in the large bowel. In the small bowel, bacteria are much more far and in between. Normally, gut bacteria are limited to 103 organisms/mL. However, SIBO is characterized by higher levels of 105 organisms/mL. This is a magnitude of a 100x difference in SIBO vs normal gut bacteria levels in a healthy individual.

The type of bacteria also matters. For example, certain bacteria can break apart bile acids which can lead to diarrhea. In contrast, another type of bacteria can produce methane gas which can lead to constipation.

What causes SIBO?

When the protective mechanisms of the small bowel that keep bacterial overgrowth at bay start to break down, SIBO can result. This can be due to multiple factors.

First, stomach acid is a main barrier to bacterial growth in the small bowel. Anything that causes low stomach acid predisposes you to SIBO. Regular movement of the gastrointestinal tract is another protective mechanism.

Low thyroid, diabetes, viral infections, abdominal surgeries, and certain medications can diminish normal flow of the gut system and lead to a stagnant environment that is conducive to SIBO.

Other risk factors for SIBO include strictures from IBD (inflammatory bowel disease), Celiac disease, alcohol use, liver disease, and loss of the valve connecting the small bowel and large bowel.

SIBO is not a benign condition. Along with the symptoms that can dampen quality of life, SIBO can also lead to

  • Inflammation of the gut lining

  • Neuropathy

  • Bone loss

  • Night blindness

  • Prolonged bleeding times

This is due to malabsorption of many key nutrients and vitamins required by the body.

Proton pump inhibitors (PPIs) affect the gut microbiome

PPIs are medications such as Prilosec and Nexium that you can find over the counter. They are in the top 10 most used drugs after they were first released in 1989. These drugs work by blocking the stomach’s natural acid production. In 2013, Prilosec was the second largest drug in term of revenue. This is not surprising given the fact that 25% of the population has GERD (reflux).

PPIs can be safely used and are very effective in preventing stomach ulcers and a precancerous condition called Barrett’s esophagus.

Nonetheless, most guidelines suggest limiting PPI use to no more than 8 weeks (sometimes 16 weeks if indicated). However, many individuals have been put on these medications indefinitely by their clinician without an attempt to investigate the root cause of their symptoms or take them off of the drug.

This is concerning because PPIs are very capable of affecting the gut and an individual’s overall health.

PPIs can decrease absorption of nutrients such as calcium, zinc, magnesium, vitamin K, and iron.

These vitamins and minerals are important in our health for maintaining bone density, bleeding times, enzyme activity, neurotransmitter production and release, and much, much more.

Furthermore, PPIs have been associated with increased risk of pneumonia, bone loss, and potentially with dementia.

PPIs also dramatically affect the health of the gut. In one study, PPI use is associated with a change in 20% of the bacteria species found in the gut. This is a more prominent affect than antibiotics have on our gut!

Learn how probiotics can help SIBO and IBS

Interestingly, more bacteria that resembles the species found in the oral cavity were found in those taking PPIs. This fact supports the notions that decreased acid production due to PPI use allows for the migration of bacteria from the mouth into the small intestine.

A large review of 23 studies with 300,000 participants, found a 65% increase risk of an infection called C. difficile. Many other gut infections are associated with PPI use as well

SIBO is associated with reflux and GERD

It just so happens that SIBO may be causing reflux/GERD in many individuals. This is found in a large association with PPI use and rates of SIBO (as we will uncover shortly). Furthermore, up to 40-64% of those with IBS have GERD, and vice versa. In another study of only 9 participants, the administration of food that exacerbates SIBO lead to relaxation of the lower esophageal sphincter (which is associated with reflux).

As mentioned before, SIBO is characterized by an overgrowth of bacteria that can cause an accumulation of abdominal gas. This gas can put pressure on the sphincter connecting the stomach and the esophagus. This can then lead to a spillage of the acidic contents from the stomach into the esophagus, thus causing GERD symptoms.

Proton pump inhibitors (PPIs) use can cause SIBO

We don’t have many great papers looking at if SIBO causes GERD per se, but we do have a lot of evidence suggesting that PPI use is associated with higher rates of SIBO.

As previously discussed, PPI use can dramatically shift the microbiome. In fact, PPIs can increase bacteria density up to 1,000 fold.

One study of 47 patients found that 53% of those taking Prilosec had SIBO. This is a much higher rate than we find in the general population of 15-20%. Another review of 11 studies including over 3,000 individuals showed that PPI use more than doubled the risk of having SIBO.

Learn how probiotics can help SIBO and IBS

Yet another study of 450 participants who had been taking PPIs for an average of 3 years points us to an association. The researchers showed 50% of those taking a PPI had SIBO, compared to 25% of those with IBS who had not taken a PPI, and 6% of healthy individuals. This means you are much more likely to have SIBO if you are taking a PPI (even more than those with IBS).

They also found that an individual was much more likely to have SIBO and more severe symptoms the longer they were on a PPI. This is enough evidence to caution my patients with extended PPI use if it’s not absolutely necessary.

A study performed in Mexico of 1,800 patients found that 45% of them started having other gut symptoms after they started taking a PPI. This is in line with another study of 5,000 people showing that PPIs lead to a 5-time increased risk of having diarrhea.

Even more interesting is that SIBO might predispose you to H. pylori infection. This is a bacterium that is associated with the development of GERD and ulcers. This further solidified the SIBO-GERD connection.

This association of PPI use and SIBO is not universal. One study of 900 patients did not show an association. However, they excluded participants in the study who had GERD and low thyroid, which we know are two very large risk factors for SIBO. This could have greatly skewed their results.

So why is there this association? It’s a chicken and egg kind of phenomenon. Does SIBO cause reflux (which leads to PPI use) or does PPI use lead to SIBO. I believe it’s both. I think that SIBO plays a large role in reflux and GERD symptoms, which leads an individual to start taking a PPI. The very use of this medication can then lead to worsening of the SIBO. This is because PPIs lower the acid content of the stomach which allows for more bacterial growth.

Strategies to lower SIBO risk if taking PPI

There are reasons that your doctor may suggest long-term use of PPIs (e.g. Barrett’s esophagus). It may be worthwhile to ask about ways you could prevent SIBO occurrence.

One study found that SIBO rates were lower if the individual was taking a prokinetic with their PPI. Examples of prokinetics include drugs such as erythromycin as well as supplements such as Iberogast and MotilPro.

A low FODMAP diet may also prove useful. You can read more about that by clicking here.

How do you know if you have SIBO?

You may be asking yourself whether or not you have SIBO and if it is contributing to your symptoms.

There’s really no consensus of what the best tool is to test for SIBO. Currently, many would argue that an endoscopy with culture of fluid is the gold standard. This is where a gastroenterologist sticks a tube down your throat and samples some of the fluid found in the small bowel to assess for bacterial content. NOT FUN!

As you can imagine, there are a lot of challenges with this approach. This includes contamination of collecting device leading to a positive result when you don’t really have SIBO, time, money, as well as the fact that most bacteria don’t grow well in culture leading to false negative results.

A breath test is another option and is one I utilize often in clinical practice. This is where the patient collects breath samples every 20 minutes for a 2-3 hour duration after drinking a small sugar solution. There are different cut offs used to assess for if you have SIBO or not, so it’s important to find a clinician who is comfortable with reading breath test results.

How to treat SIBO and alleviate GERD symptoms

After you have assessed whether or not SIBO is contributing to your GERD or gut symptoms, you can then go ahead and treat it.

Treatment usually centers around a practical dietary approach. This may include but is not limited to a low FODMAP diet which restricts fermentable carbohydrates. A semi-elemental diet can also be implemented.

Once you’ve found a diet, you can then start incorporating a trial of probiotics. Multiple studies have shown that probiotics are helpful in treating SIBO. Antimicrobial agents (both medicines and herbal options) should also be explored with your clinician.

The good news is that PPI use does not hinder SIBO treatment as one study found similar treatment success in PPI and non-PPI patients. However, another study cautioned that SIBO treatment may be slightly less effective if an individual was on a PPI for over 12 months.

This highlights the fact to not wait and get this under control before it causes more issues.

Avoid this vicious cycle

As we have uncovered, SIBO can cause GERD. This leads to PPI use which can then make the SIBO worse by lowering the acid barrier preventing bacterial overgrowth. This results more symptoms and the need for even more PPI use, and a downstream cycle ensues.

The Bottom Line

If you are dealing with reflux and GERD symptoms, you may want to assess for the potential that SIBO is causing your symptoms. As we have previously reviewed, there is a litany of research examining the association of SIBO, PPI use, and GERD. It’s important to fix the underlying root cause of your symptoms and not rely on medications to be your one and only answer. Fortunately, there is a great deal of research pointing us to potential causes of gut health issues and the interventions that should follow.

I hope you found this information useful and helpful in your journey back to a healthier and happier life.

Like what you are reading? Learn more about how to take control of your health by signing up for the "5 Minute Health Makeover" below where I coach you through 3 pivotal strategies for better health.


Resources Cited

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4. Kines, Kasia, Krupczak, Tina, 2016. Nutritional interventions for gastroesophageal reflux, irritable bowel syndrome, and hypochlorhydria: a case report.

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8. Piche T, des Varannes SB, Sacher-Huvelin S, Holst JJ, Cuber JC, Galmiche JP. Colonic fermentation influences lower esophageal sphincter function in gastroesophageal reflux disease. Gastroenterology. 2003;124(4):894-902. doi:10.1053/gast.2003.50159

9. Revaiah, P.C., Kochhar, R., Rana, S.V., Berry, N., Ashat, M., Dhaka, N., Rami Reddy, Y., Sinha, S.K., 2018. Risk of small intestinal bacterial overgrowth in patients receiving proton pump inhibitors versus proton pump inhibitors plus prokinetics. JGH Open.. doi:10.1002/jgh3.12045

10. Schmulson MJ, Frati-Munari AC. Bowel symptoms in patients that receive proton pump inhibitors. Results of a multicenter survey in Mexico. Síntomas intestinales en pacientes que reciben inhibidores de bomba de protones (IBP). Resultados de una encuesta multicéntrica en México. Rev Gastroenterol Mex. 2019;84(1):44-51. doi:10.1016/j.rgmx.2018.02.008

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