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Probiotics for SIBO: Yes or No?

You suspect you have SIBO. Maybe you were recently diagnosed with this condition. Should you be taking a probiotic? 

There is a lot of conflicting information out there. Let’s take a look at the evidence and figure out the right answer for you.

What is SIBO?

SIBO stands for small intestinal bacterial overgrowth. In a nutshell, it means you have a large amount of bacteria growing in your small intestine where they don’t belong. It is good to have a lot of beneficial bacteria in your intestinal tract. You just want most of them to be in your large intestine or colon, not in your small intestine. 

You absorb most of the nutrients from your food in your small intestine. Bacteria living in this area can break down the incoming foods. This causes the bloating, gas and abdominal pain associated with SIBO.

Small intestinal bacterial overgrowth is diagnosed by a breath test. This test measures the amount of gasses, like hydrogen and methane, that are formed when you eat certain foods. Since this is a medical diagnosis, it should be done by a doctor.

As a nutritionist I cannot diagnose you with SIBO. However I can help you with your diet to manage the symptoms. If the cause of your SIBO is nutrition-related, I may be able to help you identify and correct that as well.

What are probiotics?

Probiotics are microorganisms that are intended to provide a health benefit when they are introduced into your body. You can get them through supplements, food, or something else that you touch or eat. Many people take probiotics just for their general health. Sometimes specific strains of probiotics can be beneficial for a medical condition.

Will Probiotics Help with SIBO?

Common sense tells us that if there is an overgrowth of bacteria in the small intestine, we should not take more bacteria as a supplement. Isn’t this just fueling the fire?

A 2018 retrospective study looked at people who were suspected of having SIBO, and whether they used probiotics. Those that used probiotics within one month of the study had significantly more methane positive breath tests (1). 

It would have been interesting to know exactly what strains of probiotics the people were taking, but the study did not report this.  

On the other hand, a meta-analysis in 2017 studied probiotics for SIBO patients. The study suggested that probiotics can reduce the amount of bacteria in their gut and help with their symptoms. This is one of very few studies that actually examine probiotics with SIBO patients. Most of the research is done on people with another condition, such as IBS (2).

These are just two of many studies with conflicting results on whether probiotics can help with the symptoms of SIBO. The conflict might have to do with the fact that there are so many strains out there. 

The results you get may depend on which probiotic you take.

Which Probiotic is Best for SIBO?

There is growing research on using specific strains of probiotics to treat SIBO and other conditions. Three promising strains are Bacillus coagulans, Saccharomyces boulardii and Lactobacillus reuterii.

Bacillus Coagulans

In 2014 Khalighi and colleagues did a small study with people who had tested positive for SIBO. One group was treated with probiotic Bacillus coagulans, along with prebiotics in the form of fructo-oligosaccharides, for 15 days. This was followed by an antibiotic for another 15 days. 

The other group was only treated with an antibiotic for 15 days. The probiotic group had significantly less pain, bloating, belching and diarrhea compared to the group that just got an antibiotic.

This study demonstrates that it may be beneficial to take a probiotic regimen before or after taking antibiotics for SIBO. It doesn’t really answer whether probiotics alone can control SIBO (3).

The specific strain that they used is interesting, though. Bacillus is a soil-based, spore-forming bacteria. Bacillus has antimicrobial effects that may help decrease the bacterial count in the small intestine. This strain tends to promote beneficial microbes and suppress pathogens (4).   

Bacillus form endospores which have a tough structure that easily survives the journey through stomach acid and bile. They are more likely to reach the large intestine, where they can do a lot of beneficial things.

Bacillus clausii and Bacillus subtilis are two other strains of soil-based microbes that are used in probiotic formulas.

Saccharomyces boulardii

A study in 2020 by García-Collinot et al. found that SIBO patients who took Saccharomyces boulardii (CNCM I 745) had less exhaled hydrogen on a breath test.  This was in comparison to patients who were treated with metronidazole, an antibiotic. The probiotic-takers had a higher rate of eradicating SIBO than those on the antibiotic (5).   

I do want to note that the most common antibiotic used to treat SIBO is rifaximin, which has better results than metronidazole (9). The results might have been different if rifaximin was compared to the probiotic.

Saccharomyces boulardii is not actually a bacteria, but a type of yeast. Like the Bacillus strain, S. boulardii has antimicrobial properties that can keep down the population of harmful bacteria in the digestive tract (6).  

Lactobacillus reuteri

Lactobacillus reuterii is a different species from the spore-based bacteria we talked about earlier.

A four week regimen of Lactobacillus reuterii (DSM 17938) significantly decreased methane production in a small study of middle-aged females. Over half the subjects showed no methane production on their breath tests at the end of the study. They also had less constipation.

Like Bacillus and Saccharomyces, the L. reuteri bacterial strain can help to balance the population of microbes in the gut. Its mild antimicrobial action keeps harmful bacteria under control while beneficial bacteria is allowed to grow (7).

Getting at the Root Cause of SIBO

The research is still very young in this area. There have not been many studies using probiotics in patients who actually have SIBO. The studies that have been done tend to be very small. 

That is why I would recommend trying other methods to get relief from your symptoms before going to a probiotic.

If you do decide to take a probiotic, make sure to do it slowly. Keep an eye out to see whether it will improve or exacerbate your symptoms. 

A more important thing to think about is this: why do you have SIBO in the first place? There will be a root cause or underlying condition that allowed those bacteria to flourish where they did not belong.

It is important to fix this condition. Otherwise your bacterial overgrowth will continue to come back as soon as you stop your treatment regimen.


Dysmotility just means poor movement in your digestive system. A healthy gut will propel food along so that it doesn’t stay in the small intestine.

This happens through a series of muscle movements called the migrating motor complex (MMC). The MMC sweeps food debris and bacteria down into the colon in between your meals.

You can improve a dysfunctional migrating motor complex with food and lifestyle changes.


Hypochlorhydria means low stomach acid. One of the functions of stomach acid is to kill excess amounts of bacteria that are in your upper digestive tract. 

A poor diet, age, or certain medications can cause low stomach acid. You can take a test at home to see if your stomach acid is low.

Inflammation in the Digestive Tract

Any condition that causes inflammation in the digestive tract can set you up for a bacterial overgrowth situation. These include things like pancreatitis, inflammatory bowel disease, or prior surgery on your bowel. Your doctor can monitor and treat these conditions. 

Structural Abnormalities

Structural abnormalities can also be responsible for SIBO. For example, if the valve between the small intestine and the colon is not functional, bacteria can leak up into the small intestine (8). 

However, conditions like this are out of the scope of a nutritionist. Your doctor is the one who can diagnose and treat you.

PPI Usage

Research tells us there is an association between the use of  PPI (proton pump inhibitors) and the development of SIBO. This makes perfect sense. One of the main jobs of stomach acid is to keep bacteria levels under control in the stomach.

Do not stop taking PPIs prescribed by your doctor! However you can work with your doctor and your nutritionist to manage your SIBO symptoms.

The Last Word

You might be confused about whether you should take a probiotic for SIBO. The research is kind of all over the place. Some studies show a benefit, and others show that it might make SIBO worse.

SIBO is caused by an overgrowth of bacteria. It certainly doesn’t make sense to add more bacteria to the mix!

However evidence is emerging that specific microbe strains might actually benefit a person with SIBO. Three promising microbes are Bacillus coagulans, Saccharomyces boulardii and Lactobacillus reuteri.

The research is still scanty. Studies are small, and most subjects are people who are being treated for other conditions like IBS. If you decide to try one of these probiotics, run it by your doctor first. Take it slow and watch to see if it helps or hurts your symptoms.

Don’t forget that something caused your SIBO in the first place. It could be poor motility in the digestive system, low stomach acid, medications or structural problems in your GI tract. 

You can improve poor motility and low stomach acid when you eat the right foods and make simple lifestyle changes. Would you like to learn more? Just click the button below to find out how.

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