Let me preface this by saying that taking probiotics for SIBO is not only a controversial issue, but is very complex.  No two cases of SIBO are exactly the same.  Considering that there are dozens of popular probiotic strains (not to mention the many probiotics which aren’t popularly marketed), it is no wonder that SIBO studies and users have mixed results with probiotics.

However, probiotics can be a very valuable part of SIBO treatment and some medical practitioners ever say they are a necessary part of SIBO treatment – so long as the right probiotics are chosen.

What Is SIBO?

Let’s start with a little review.  Small Intestinal Bacterial Overgrowth (SIBO) is a condition in which you have too much and/or the wrong type of bacteria in your gut.  The problem isn’t like an infection of strep throat where one “bad” bacteria has gotten into your throat.  The problem is that the 100 trillion bacteria which live in your gut (yes, there really is that many bacteria in just your intestines!) have become imbalanced.  This is known as gut flora dysbiosis.

As registered dietician Tamara Duker Freuman wrote about SIBO in US News and World Report:

“A common misconception is that SIBO involves overgrowth of ‘bad’ or ‘disease causing’ bacteria…In reality, there’s nothing inherently ‘bad’ about the bacteria in SIBO other than that they’re colonizing the wrong neighborhood; rather, SIBO is typically caused by good bacteria living in an inappropriate location.”

To see if you have SIBO, you will need to take a hydrogen/methane breath test.


Good news! There are now SIBO breath tests that you can order directly without a doctor’s order! While I’m a HUGE fan of having a doctor’s guidance, I understand the need to know whether you have SIBO or not before you invest in a practitioner.

You can order the test directly and it will be sent to your home with instructions on how to take it and how to send it back and get your results!

What Are Probiotics?

As defined by The World Health Organization, probiotics are “live micro-organisms which, when administered in adequate amounts, confer a health benefit on the host.”

The probiotic industry is expected to exceed $64 billion by 2023 thanks to all the trendy yogurts and supplements.1 I’ve even seen probiotic peanut butter being sold!

There are definitely proven benefits of taking probiotics – including for SIBO – but I mention the market size as a reminder to be wary.  No probiotic is a magic bullet that will cure all of your problems!

Probiotics Could Be Triggering Your SIBO

Remember that SIBO isn’t caused by “bad” bacteria.  Even “good” bacteria can cause SIBO if they grow out of control in your gut.  Thus, taking probiotics could add fuel to the fire which is SIBO.

However, the problem with taking probiotics for SIBO usually isn’t that you’ve got too much of the bacteria strain in that particular probiotic.  Rather, the issue is that most probiotics contain prebiotics.

Bacteria, like all living things, need to eat something.  To help the probiotic repopulate in your gut, many probiotic manufacturers add prebiotics – which is basically just food for the probiotics to eat so they can reproduce.

The problem with prebiotics is that other bacteria will also feed off of them.  If you’ve got SIBO, the last thing you want is to feed the bacteria in your gut!  This would counter all of the work you’ve done by eating a gut-friendly diet (read this post about The Best Diet for SIBO).

In addition to prebiotics, some probiotics contain ingredients which trigger SIBO responses.  On her website here, Functional Medicine Nutritionist Angela Pifer gives some examples of these ingredients which are found in popular probiotics:

  • Jarro Dophilus: Contains maltodextrin, tapioca starch, dairy and soy
  • Florastor: Contains lactose
  • Align: Contains lactose
  • Culturelle: Contains inulin
  • Jarrow Ideal Bowel Support: Contains potato starch and soy
  • Pears YB: Contains pectin
  • Probio Pure’s: Contains tapioca starch

As Pifer says, taking any of these probiotics while you have SIBO would work against treatment.  They’d just fuel the overgrowth of bacteria in the small intestines and make it harder to restore balance.

How (the Right) Probiotics Help SIBO

Just because some probiotics might trigger SIBO, it doesn’t mean that you should dismiss all probiotics immediately.  Probiotics can be indispensable in helping you correct dysbiosis (unbalanced gut flora) after treatment – particularly treatment with antibiotics or herbal antibiotics for SIBO.3

There are three ways that probiotics could help fix dysbiosis and treat SIBO:

  1. Probiotics help modulate the gut’s immune system
  2. Probiotics produce anti-microbial compounds that help illuminate pathogens. These compounds are vital for keeping levels of “bad” bacteria under control and preventing and treating dysbiosis.
  3. Probiotics strengthen the gut mucosal barrier and prevent pathologic bacteria from clinging to the GI tract walls.
  4. Probiotics improve motility (read more about motility here).4

Scientific Studies on Probiotics for SIBO

It was only recently that doctors became aware of SIBO, so research is still in its infancy.  Unfortunately, studies have had very mixed results.

Note that 84% of IBS cases are actually SIBO, and there have been numerous studies about using probiotics for IBS.  However, as with the SIBO studies, these studies had very mixed results.  Again, don’t let this dissuade you from probiotics completely.  As one researcher who tried to do a meta-analysis of IBS researcher said, the studies were so diverse in terms of probiotic strains and concentration used, that it was impossible to determine efficacy.6

Here are a few studies which showed a positive result when using probiotics for SIBO:

  • A pilot study compared probiotics to antibiotic treatment for SIBO. The group taking probiotics had an 82% improvement compared to 52% for the antibiotic group.  Strains used were Lactobacillus casei, Lactobacillus plantarum, Streptococcus faecalis and Bifidobacterium brevis. Both groups also were on a diet that limited legumes, alcohol, leafy greens and dairy. (Source)
  • A study had patients take a 6-week course of Lactobacillus casei. 64% of the patients had a negative breath test afterwards. (Source)
  • A study gave SIBO patients two billion spores of Bacillus clausii 3x per day for 1 month. 47% of the patients had negative breath tests afterwards. (Source)

How to Take Probiotics for SIBO

There is no established medical consensus on probiotics for SIBO, and each case varies.  However, SIBO experts do have some practical advice for how to take probiotics for treating SIBO.

  • Avoid Probiotics with Prebiotics: Prebiotics can feed the bacteria in your intestines and worsen your SIBO.
  • Avoid Probiotics with Additives: Likewise, these additives can feed bacteria in the gut. Avoid additives which aren’t advised while on the SIBO diet (such as lactose, starches, and soy).
  • Start Small! Pifer has her patients start with a dose of less than a million flora. Most probiotics have billions of flora per capsule. You will need to open the capsule in order to take the partial dose.  If you tolerate the probiotic, gradually increase to the full dosage.
  • If you have reactions to the probiotic, stop taking it: Reactions are often in the first few hours after taking the probiotic.
  • Find a probiotic which makes you feel better and stick with it: Everyone is different. What works for one person’s SIBO might not work for yours.  So stick to the probiotics which do work for you.
  • Use a supplement instead of fermented foods: Many people with SIBO react poorly to lacto-based probiotics which are found in fermented foods – especially if histamine intolerance is an issue.
  • Time your probiotics right: At the beginning of treatment, some people do not tolerate any probiotics. That doesn’t mean you should avoid probiotics forever.  Consider taking the probiotics after a course of antibiotics or herbal antibiotics to help restore gut flora.
  • If you can’t tolerate any probiotics: Then focus on repairing your MMC and try reintroducing probiotics later.12,13

Best Probiotics for SIBO

I will remind you again that everyone’s SIBO is different.  Probiotics which work for one person might not work for you.  Start slow with low-dosages of the probiotics to see if they make you feel better or worse. If it works, stick with it.  If it doesn’t, try another strain of probiotics.  And, as always, check with your doctor.  15 , 16, 17, 18, 19

1. Saccharomyces boulardii

This is actually a type of yeast and not bacteria. It is the only yeast which is considered beneficial enough to be considered a probiotic. It helps fight off pathogenic strains of bacteria and reduces inflammation. Note that S. boulardii does not colonize the gut so it will need to be taken continuously and it is recommended to take it with a bacteria which will colonize the gut.  Thanks to Dr. Alison Ramsden for letting me know about this brand of saccharomyces boulardii which doesn’t contain any prebiotics. You can buy it here.

2. Bifidobacterium infantis 35624

This probiotic is well-tested and shown to reduce abdominal pain, bloating, and bowel movement difficulty. Results suggest that it works by having an immune-modulating role. This specific strain is a bit difficult to find.  However, Klaire Labs (a great company!) does make one probiotic with it and it has no prebiotics or other off-limit ingredients.  It is called Lactoprime Plus and you can buy it here.

3. Bifidus lactis

This probiotic is shown to enhance the immune system, reduce occurrence of antibiotic-associated diarrhea, and support proper bowel movements.  Kirkman makes a good probiotic with this strain.  You can buy it here.

4. Lactobacillus plantarum

This probiotic is shown to reduce bloating, normalizes stool frequency, relieve abdominal pain, and improve IBS symptoms, prevent overproduction of yeast, and reduce bacterial translocation.  This is also found in the same supplement which has s. boulardii.  You can buy it here


5. Bacillus Indicus (HU36TM)

Better known by its brand name MegaSporeBiotic, this is a soil-based probiotic which many SIBO and IBS sufferers have reported success with. Unfortunately, it is only available with a doctor’s prescription. Prescript-Assist is another soil-based probiotic which many people report success with and you don’t need a prescription for it. Note that it does contain prebiotics though, so you’ll need to see how you react to it or just go with one of the other prebiotics.

Disclaimer: None of these statements have been approved by the FDA.  While some scientific evidence does exist that shows probiotics might help SIBO, there is no conclusive evidence.  Talk to your doctor before taking any probiotics for SIBO.

If you are ready to be done with SIBO once and for all, download the eBook The SIBO Solution.  You’ll find detailed information on SIBO causes, treatment protocols, diets for SIBO and even recipes for SIBO.  Buy The SIBO Solution Here.

The SIBO Solution

Have you tried probiotics for SIBO? I’d love to hear what worked/didn’t work for you!

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Sylvie McCracken is a former celebrity assistant in Hollywood turned full time entrepreneur currently living in Ashland, Oregon with her kids. She writes about treating and preventing health conditions with real food and natural remedies, as well as anything else she feels like writing about because she's a rebel like that. ? he also mentors health professionals turned entrepreneurs on her other site, SylvieMcCracken.com