Best probiotics for SIBO

Updated on :

By Dr.HMT

In recent years, probiotics have gained public attention for their ability to improve gut health and treat gastrointestinal diseases. This article discusses the top probiotic strains for managing SIBO, a common gastrointestinal disorder, and provides an overview of current research in this field.

What is small intestinal bacterial overgrowth (SIBO)?

SIBO is an overgrowth of bacteria in the small intestine. The normal small intestine contains fewer than 104/ml organisms. In SIBO, there may be 108-1010/ml organisms, most of which are normally found in the colon.

When an abnormally large number of bacteria take root in the small intestine, there is increased bacterial fermentation of food. The process produces excessive intestinal gas causing unpleasant GI symptoms.

Moreover, bacterial overgrowth can lead to small intestinal mucosal inflammation, and flattening of intestinal villi (specialized for absorptive function) in the long term. This prevents optimal absorption of nutrients and can lead to malnutrition.

What are the symptoms of SIBO?

SIBO symptoms are commonly due to increased bacteria fermentation of food in the small intestine and malnutrition.

  • Excessive gas 
  • Bloating 
  • Nausea 
  • Abdominal pain
  • Change in bowel habits (Diarrhea or constipation)
  • Unintentional weight loss
  • Anemia
  • Vitamins and minerals deficiencies

What causes SIBO?

Disorders that impair the normal physiological mechanisms controlling bacterial proliferation in the intestine predispose to bacterial overgrowth.


Loss of gastric acidity
Removal of all or part of the stomach (gastrectomy), long-term use of acid-lowering medications (PPI)


Impaired intestinal motility
Diabetes (nerve dysfunction can disrupt intestinal motility), post radiation enteropathy, scleroderma( due to weakening of gut muscles)

Structural abnormalities 
Surgical blind loop, extensive small bowel resection, diverticulosis, intestinal obstruction

Impaired immune function
Any form of immunodeficiency including AIDS

Are probiotics helpful for SIBO?

Yes. Probiotics are front liners of defense against luminal pathogens. They can help SIBO by the following mechanisms.

  1. Antimicrobial properties
  • Certain probiotics can produce antimicrobial proteins called bacteriocins. For instance, research has shown that bacteriocins produced by lactobacillus species can suppress the growth of harmful bacteria like E.coli.
  • Probiotics also engage in competition with pathogenic microbes for nutrients.
  1. Restore balance in the gut microbiota

Probiotics deliver beneficial gut bacteria which replace the harmful microbes and help restore a healthy microbiota.

  1. Strengthen and heal the inflamed gut lining

Probiotic bacteria eat dietary fiber and release beneficial metabolites called short-chain fatty acids. SCFAs are a prime energy source for gut lining cells and they strengthen the gut barrier function.

  1. Immunomodulation

Probiotics help to reduce intestinal inflammation by modulating the immune response. They have been shown to decrease proinflammatory cytokines (markers of inflammation).

What does the research tell us about probiotics for SIBO?

A meta-analysis summarizing 18 clinical trials concluded that probiotics are effective in reducing the bacterial burden in SIBO patients and alleviating their symptoms.

Probiotics may also enhance the effectiveness of antibiotics as demonstrated in a study where patients treated with rifaximin along with probiotics had greater improvement in their symptoms as opposed to antibiotics alone.

Although there is so much more to explore in this area of research, the evidence so far shows that probiotics can be an effective strategy for treating SIBO.

The best probiotics for SIBO treatment

Saccharomyces boulardii (probiotic yeast)

In a clinical study of 40 patients diagnosed with SIBO, patients who took Saccharomyces boulardii either alone or in conjunction with antibiotics had a significant reduction in diarrhea, abdominal pain, and bloating compared to antibiotics alone. Moreover, the Saccharomyces boulardii group had the lowest level of adverse effects from treatment.

Soil-based probiotics (Bacillus species)

Soil-based probiotics are spore-forming microorganisms that populate soil. They have shown promise in SIBO. Studies have found that supplementing Bacillus coagulans alongside an antibiotic regimen significantly decreases SIBO symptoms such as flatulence, abdominal pain and diarrhea. Additionally, testing for SIBO turns negative in 93.3% of those taking the probiotic compared to 66.7 percent of the control group.

Lactobacillus reuteri

Reuterin produced by L.reuteri is a potent antimicrobial against the main bugs that accompany SIBO, like E. coli and Klebsiella. A recent study has found that the DSM17938 strain of Lactobacillus reuteri, can significantly reduce the risk of SIBO in patients taking proton pump inhibitors (PPI).

Bifidobacterium bifidum, B.lactis and B.longum

In SIBO-positive cancer patients, probiotic Bifidobacterium therapy for 4 weeks has been shown to combat SIBO and alleviate some of their gastrointestinal symptoms. 

Are probiotics safe for people with SIBO?

Probiotics are generally recognized as safe, and a smart choice of the right probiotics will help you recover from SIBO more quickly.

However, a recent study has also shown that probiotics may provoke symptoms among SIBO patients including gas, bloating, and brain fogginess. In the study, probiotic cessation, and a course of antibiotics, resolved brain fogginess while improving other gastrointestinal symptoms. 

This suggests that not all probiotics are of equal efficacy, especially in the case of SIBO and thus should be used under care of medical professionals.

Final verdict

The common question I got asked from my SIBO patients is “ isn’t the probiotic adding more bacteria to bacteria overgrowth?”

If you are adding some random probiotics, they could be adding fuel to SIBO fire. But, studies have proved that a good probiotic protocol can help maintain intestinal homeostasis and is worthy to consider adding into your regimen if you have SIBO.

The probiotics I have mentioned above generally work best for SIBO. However, SIBO is a tricky digestive condition, and every SIBO patient has a unique gut microbiome. So, I recommend going for it under the care of an experienced practitioner.