The Best Probiotics for SIBO: Strains and Brands

Image of white probiotic capsules and a leaf on a white background with wording The Best Probiotics for SIBO by The Healthy RD

Probiotics and SIBO (small intestinal bacterial overgrowth) are getting a lot of attention in research, so getting the best probiotics for SIBO is the aim of this post. 

Here, learn about the best Lactobacillus, Bacillus, and Saccharomyces strains to choose from for SIBO. 

But when it comes to probiotics, SIBO is a bit of a controversial issue.  We will delve into that too. Also, learn how to be a smart consumer of probiotics if you have SIBO issues. 

Overview of best probiotic strains for SIBO 

Some practitioners believe that using antibiotics, a low FODMAP diet, and avoiding probiotic foods and probiotics is the standard treatment for SIBO.  

And yet, research shows that several strains of probiotics help with SIBO digestive symptoms. What is more, certain kinds of probiotics can even help eradicate SIBO.  

Because of this, some experts in the field of SIBO are now recommending using certain strains of probiotics for SIBO treatment.  

These strains include:

  • Bacillus coagulans
  • Bacillus subtilis
  • Bacillus clausii
  • Saccharomyces boulardii
  • Lactobacillus rhamnosus
  • Lactobacillus reuteri

Finding probiotic supplements that contain a broad spectrum of these strains is ideal in many cases. But as an individual, you may need to try single strains first to see if you are on the right track.  

Here are some interesting research findings that have been done on some of these strains and SIBO patients.

Related post: 7 of the Best Probiotics for UTI Prevention + Lifestyle Tips (

Soil-based strains for SIBO

Soil-based probiotics are types of spores that are found in healthy soil. 

Strains of probiotics that are found in the soil include Bacillus coagulans, Bacillus subtilis, and Bacillus clausii.  These strains have a number of beneficial effects for people with SIBO.  

One of the best parts about soil-based probiotics is that they colonize in the large intestine and don’t grow in the small intestine. And even more importantly, numerous studies show that they help reduce SIBO symptoms. 

Bacillus coagulans help the bacteria in the large intestine colonize, promote immune stimulation and even help to decrease the risk of kidney issues.  Early research also shows that this strain helped 93 percent of people by resulting in a negative hydrogen breath test in people with SIBO

Bacillus subtilis helps the body to produce over 12 natural antibiotics to keep your gut free of harmful bacteria. As part of a broad-spectrum probiotic, Bacillus subtilis helped improve the SIBO cure rate and reduced SIBO symptoms according to recent research.  It also helps to ferment vitamin K in the gut. Last but not least, it supports gut repair by increasing IgA and butyrate as shown in a clinical trial.

Bacillus clausii helps make IgA which is a gut-repairing type of immunoglobulin. It has also successfully been used to help treat SIBO. 

Lactobacillus reuteri

Another probiotic strain called Lactobacillus reuteri is one of the best probiotics for methane SIBO because it is clinically proven to reduce methane in people with SIBO [R]. 

It also reduces symptoms of constipation. 

Research also shows that Lactobacillus reuteri helps fight harmful bacteria like E.coli and other opportunistic bugs that can be present in people with SIBO.  

Lactobacillus reuteri is also particularly helpful in people who take stomach acid medications. 

Related post: Best Probiotics for Kids: How to Choose

Saccharomyces boulardii for SIBO

Saccharomyces boulardii is a live yeast type of probiotic. It has been used for decades safely for many purposes.

It does many things, including helping the immune system and keeping the gut in balance. Additionally, it helps to strengthen the gut lining according to clinical research. 

S. Boulardii also helps the body absorb nutrients. This is an important feature because people with SIBO have a reduced ability to absorb nutrients. 

Further, S. Boulardii reduces SIBO symptoms, including diarrhea, abdominal pain, bloating, and reduced breath hydrogen levels. Even more, Saccharomyces helped eradicate SIBO in this study.  For all of these reasons, it is often considered the best probiotic strain for SIBO. 

Saccharomyces boulardii is a very appealing  strain for people with SIBO because it doesn’t overgrow in the small bowel. It helps with so many intestinal symptoms, including diarrhea, bloating, and abdominal pain.  What is more, it even improves nutrient absorption. 

For SIBO treatment, probiotics like S. boulardii have minimal risks.  Just make sure that you choose a reputable brand with a live and active culture of Saccharomyces boulardii. 

Lactobacillus rhamnosus

In a recent study, Lactobacillus rhamnosus helped reduce IBS symptoms which are closely related to SIBO.  

Often, IBS and SIBO overlap according to a clinical study in the World Journal of Gastroenterology

Related post: The Best Probiotics for Acid Reflux in 2021 (

SIBO probiotics to avoid

Some forms of probiotic strains, including some kinds of lactic acid bacteria and bifidobacterium, cause the body to increase SIBO symptoms, at least in some people.  These strains include [R]:

  • Lactobacillus casei 
  • Lactobacillus bulgaricus 
  • Bifidobacterium lactis –increases methane, but some studies do show it helps SIBO.  Caution if you have high methane levels. 
  • Bifidobacterium infantis–increases methane

Bifidobacterium infantis (Align brand) may increase the chances that you have a positive methane test, so this strain may be best to be avoided if you have SIBO. 

While you may feel fine taking these probiotic strains, they also may temporarily ramp up some of your SIBO symptoms. 

Related post: Who Should Not Take Probiotics + Important Benefits

Best probiotics for SIBO brand criteria

Only the best probiotics for SIBO strains make this list.  The other criteria for the selection include:

  • GMP certified, which means third-party-inspected
  • Highly rated probiotics with greater than 4.5-star reviews by over 100 reviewers
  • Contains strains that are good for SIBO
  • Free of methane-producing bacteria

Best probiotics for SIBO: brands

It is challenging to sort through all the brands of probiotics to determine if they have the right probiotic strains for both SIBO.   

To help you with that, here are some top-rated brands that have probiotic strains shown in research to help.

While more and more research is showing that probiotics are beneficial for SIBO, you will want to be careful about the strains you choose.

Especially watch out for the types of probiotics you take if you also have histamine intolerance or allergies as well. 

This is because some probiotics can increase histamine in your gut, and you definitely don’t want that if you have histamine intolerance.

By the way, none of these brands have probiotics that stimulate histamine release. 

Best Brands

Ancient Nutrition SBO – Probiotic blend has 25 billion CFUs including Saccharomyces boulardii, Bacillus coagulans, Bacillus clausii, and Bacillus subtilis.  Because it contains an ideal blend of strains it is considered among the best probiotics for SIBO. It also contains healthy adaptogenic mushrooms that help support a healthy microbiome. Third-party tested and GMP certified.

Image of Florastor for the Best probiotics for SIBO post by The Healthyrd

Florastor is a reputable brand of Saccharomyces boulardii that has over 2000 positive reviews.  It even contains the researched strain of Saccharomyces boulardii lyo CNCM I-745.  This strain helps with many digestive conditions and is also supportive of healing from histamine issues. If you are on a budget, this is the best value for your money.  It can be safely taken if you have candida or yeast overgrowth too.  Often, it is one of the easiest-to-tolerate probiotics out there.  Certified GMP product and third-party inspection.

Primal Earth Probiotic by Amy Myers MD is among the best probiotics for SIBO because it contains 3 soil-based probiotic strains.  The ingredients are Bacillus subtilis, Bacillus coagulans, and Bacillus clausii, which are clinically proven strains for reducing SIBO. This probiotic has over 600 5-star reviews that are positive for supporting overall health and gut balance.  Great for people who want the best soil-based probiotic for SIBO that also helps reduce histamine intolerance. Contains a 30-day supply per bottle. GMP-certified company with independent third-party testing.

Biogaia protectis supplement by The Healthy RD

BioGaia Protectis chewable tablets are geared towards, children, toddlers, and teens because they are chewable and in a lower dose. They contain the research-validated strain Lactobacillus Reuteri for reducing SIBO symptoms. It comes in a lemon-lime flavor and contains 100 million CFU of Lactobacillus Reuteri DSM 17938. GMP-certified company with third-party testing.

Mega Spore Biotic

Mega Spore Biotic is a brand that has been clinically studied to reduce symptoms of irritable bowel syndrome [R]. This probiotic is clinically proven to help SIBO and is in my opinion, the best probiotic for small intestine health. This is among the best brands of spore probiotics for irritable bowel syndrome because this specific product has been studied clinically for this condition. Contains the probiotics Bacillus coagulans, Bacillus clausii, Bacillus licheniformis, Bacillus subtilis, and Bacillus indicus.  It is also quality-controlled because it is GMP-certified with third-party testing. Also available on Amazon

Image of Microbiome Plus Gastrointestinal for the Best Probiotics for SIBO post by The Healthy RD

Microbiome Plus is a Lactobacillus reuteri supplement for adults with rave reviews and is very well-tolerated. It supports overall gut health and helps many people reduce their cholesterol levels as well. This strain is generally recognized as safe by the FDA as well. This company is GMP-certified.

What is SIBO?

SIBO, or small intestinal bacterial overgrowth, is a condition where excess bacteria grow in the small intestine where they normally shouldn’t grow.  

Not only does this make people uncomfortable, but these bacteria also begin to digest food particles and rob the body of nutrients. 

These bacteria can ferment your foods in the wrong places and cause pain, bloating, and more. 

Small intestinal bacterial overgrowth is also under the broad umbrella of gut imbalance. 

According to research in the Journal of Clinical Gastroenterology and Hepatology, as many as half of the people with irritable bowel syndrome have SIBO too.  

You can find out if you have SIBO by getting a hydrogen and methane breath test from your healthcare provider.  Alternatively, you can find out if you have SIBO based on symptoms as well.  

Related: How to Reduce SIBO Die Off Symptoms + Prevention

Symptoms of SIBO

SIBO symptoms are often quite obvious because one of the main symptoms is bloating up like a balloon after meals.  This can feel quite uncomfortable.  

In fact, common symptoms of this condition include: 

  • Excessive gas (from hydrogen and methane gas) 
  • Bloating 
  • Nausea 
  • Abdominal pain 
  • Intestinal inflammation 
  • Fatigue-due to reduced nutrient absorption

As you can see, these are very similar symptoms to IBS because the two conditions are closely related. 

These also share similarities with symptoms of histamine intolerance too.  

What causes SIBO?

SIBO is generally related to common issues in today’s world. 

These can include:

  • Reduced stomach acid from proton pump inhibitors or aging 
  • Constipation, food intolerances, or gastrointestinal surgeries
  • Antibiotic use

Related: Do you have low stomach acid? Signs and simple remedies

Why use probiotics for SIBO?

Even though it seems contradictory to use probiotics when dealing with SIBO, certain strains of bacteria are beneficial as reviewed above. 

Think of it like this: the good probiotic bacteria can help fight the bad bacteria and also help your immune system work.  

For example, an impressive review of 18 clinical trials found that probiotics can be useful in helping to treat SIBO

In summary, these probiotics help to:

  • Reduce bacterial overgrowth 
  • Improve the gut lining 
  • Support a healthy immune system 
  • Can help prevent diarrhea
  • Reduce constipation symptoms

Additionally, probiotics help IBS patients in numerous clinical studies, and a good majority of people with IBS suffer silently from SIBO. 

Related post: The Best Probiotics for Anxiety and OCD

Are probiotics safe for people with SIBO?

Probiotics are generally recognized as safe, and if you choose the right strains of probiotics like Saccharomyces boulardii, soil-based probiotics, and Lactobacillus reuteri, you probably will recover from SIBO more quickly. 

Additionally, most probiotics, including soil probiotics, have minimal to no side effects. This is because they are natural and beneficial bacteria. 

Occasionally, probiotics are related to mild digestive issues. This can include gas, bloating, and changes in bowel movements.  

However, these are usually short-term and go away after a week or so.

But, be sure to always check with your doctor or healthcare provider before taking any new probiotics. 

Best probiotic for SIBO summary

Many types of probiotics can help with SIBO. Some practitioners recommend avoiding probiotics. But based on the ongoing research showing that probiotics help SIBO, avoiding probiotics seems silly. 

Just make sure to carefully read your probiotic labels or choose the brands researched above. 

Try to also include fermented foods whenever possible to gain the best array of probiotics and to enhance your body’s ability to digest these foods and nutrients. 

Disclaimer – The information contained on this blog, website, and related content is of a general nature and not regulated by the FDA. They are not intended to treat, diagnose, or give specific medical advice. While all content is written by a registered dietitian and strives to provide only accurate, scientific-based information, your specific health needs may or may not apply to the content contained on this website and related content. It is not intended to diagnose or treat any specific medical condition. All content is copyrighted and must be used only with permission and citation to


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