What’s the Best Probiotic for SIBO?

A passing gut issue can ruin your day. Besides the time spent in the bathroom, there’s all the bloating and gas that can kill your physical discomfort and push your self-consciousness into overdrive. And imagine if the gut problem weren’t a passing thing but rather of indefinite duration, like with SIBO. It’s enough to make a person desperate for a solution in the supplements aisle, where more than a few probiotics offer the potential for relief.

As is the case with all supplements, some SIBO probiotics are better than others. The best ones are no guaranteed remedy, and you’ll want to consult a medical provider as to their suitability for your recovery, but the quality they have in common is they contain specific probiotic microorganisms that have acquitted themselves relatively well in clinical research.

See our summary of recommendations just below for the rundown. Then read further to see how we made our selections.

Summary of recommendations

• Best single-strain probiotic: Florastor Dual Action Probiotic
• Best multi-strain probiotic: Microbiome Labs RestorFlora
• Best for methane SIBO: BioGaia Gastrus Probiotic Chewables
• Lowest up-front cost: NOW Foods Saccharomyces Boulardii

Over the past two decades, Innerbody Research has helped tens of millions of readers make more informed decisions about staying healthy and living healthier lifestyles.

This guide to the best SIBO probiotics synthesizes both the theoretical and the practical knowledge that we gained over nearly 100 hours of research effort. We first searched and studied the literature on SIBO and the role that probiotics may play in treating it. We then applied this knowledge to identifying probiotic supplements whose formulations aligned with direct or tangential clinical studies. With a shortlist in place, we finally ordered the market’s best SIBO probiotics ourselves so that we could speak to the customer experience.

Additionally, like all health-related content on this website, this guide was thoroughly vetted by one or more members of our Medical Review Board for accuracy and will continue to be monitored for updates by our editorial team.

We selected the products in this guide based on three criteria that are the likeliest to move consumer decisions:

• Effectiveness: How well a particular supplement’s formulation aligns with the current scientific literature on probiotic therapy for SIBO
• Safety: How minimal a risk a supplement might pose to people with SIBO
• Cost: How sustainably affordable a supplement is compared with competitors

Here’s how our top recommendations rated in each category.

Effectiveness

Advantage: Florastor Dual Action Probiotic

In the current body of research on SIBO probiotics, one strain stands out for having withstood the most scrutiny, so far, in direct SIBO studies: Saccharomyces boulardii CNCM I-745. This is the strain that led to an 80% SIBO elimination rate in one randomized clinical trial and decreased hydrogen excretion better than placebo in a separate study.15 21 It’s also the strain that runs solo in Florastor Dual Action Probiotic, in what appears to be a clinically relevant dose,23 24 and the brand itself has been tested in at least one successful trial of a product containing the strain.22 When all such factors are considered, Florastor rises above the competition.

Another of our recommendations, NOW Foods, uses S. boulardii as well, but it doesn’t identify the strain. The species in general is well-studied for gut health improvements, but the lack of a strain designation means we can’t be more specific than that. It’s rather an entry-level product for people who prioritize an ultra-low price tag.

Our other two recs, Microbiome Labs and BioGaia, are excellent in their own rights, but they either lack direct SIBO testing or are better suited for a narrower cohort of SIBO patients. We discuss their strengths in their respective brand sections near the end of this guide.

Safety

Advantage: BioGaia Gastrus Probiotic Chewables

While S. boulardii has the most research support behind it, it’s also a theoretically risky option since it has been linked to a life-threatening infection called Saccharomyces fungemia.19 Although the risk principally relates to people with immunocompromise, critical illness, or indwelling catheters, it’s a serious factor that brings down the species’ value in terms of safety.

But Limosilactobacillus reuteri poses no such risk. In fact, it boasts a fair bit of human safety data. A 2024 randomized clinical trial, which administered L. reuteri DSM 17938 and ATCC PTA 6475, found that the frequency of adverse events was similar between the intervention and placebo groups,35 suggesting that the two strains hardly differed from baseline in terms of their safety profiles. The same two strains are those used in BioGaia Gastrus Probiotic Chewables.

We want to make clear that, for the overwhelming majority of potential users, the infection risk associated with S. boulardii is very small. Yet when you compare the risk with L. reuteri, it’s the latter species that presents as the more reassuring therapeutic option. And when you compare BioGaia’s L. reuteri strains with the three Bacillus ones in Microbiome Labs, you find that only BioGaia’s exact combination has been evaluated for safety. BioGaia, therefore, stands out as the safest recommendation in our guide.

Cost

Advantage: Microbiome Labs RestorFlora

Microbiome Labs isn’t the lowest-cost option in our guide, or even the most cost-effective, but with its combination of a complex formulation and relatively large quantity, it offers the most might for your money. This table illustrates:

At its subscription level, Microbiome Labs costs only $0.02 more per serving than NOW Foods while providing four strain-specific probiotics as opposed to NOW Foods’ one nonspecific S. boulardii species. Moreover, Microbiome’s per-serving cost range is lower than that of BioGaia or Florastor, which also have fewer strains in their formulations.

That being said, if the up-front cost is your primary constraint, then NOW Foods is the obvious choice. Even its higher-quantity offering costs less than its Microbiome Labs and BioGaia counterparts, while Florastor simply costs too much more per serving to compete seriously in this category

Before we get into the science behind SIBO and SIBO probiotics, check out this quick-reference table comparing our recommendations in key categories:

Small intestinal bacterial overgrowth (SIBO) is a bowel disorder in which the small intestine plays host to an abnormal quantity or combination of bacteria.

Ordinarily it’s the colon that houses the most microorganisms, partly because food residues move through it more slowly, giving bacteria more time to multiply. And that’s fine, because with its dual-layer mucus barrier, the colon is adapted to accommodate large bacterial loads.1 With the small intestine, that isn’t the case; it’s supposed to assume a different role involving digestion and nutrient absorption, processes that can be disrupted by excessive bacterial growth or an abnormal bacterial composition.2

Indeed, SIBO can throw a wrench into your digestive processes. During normal digestion, the small intestine absorbs most nutrients before food reaches the colon, and the colon is where microbes ferment the carbohydrates and fibers the body did not digest.2 But in SIBO, the food is besieged by fermenting bacteria much earlier, potentially impairing nutrient absorption and producing gases that stretch the intestine, contributing to symptoms such as:3

• Bloating
• Belching
• Cramps
• Diarrhea
• Distension
• Gas
• Nausea
• Stomach upset
• Uncomfortable fullness after eating

Some bacteria may even alter the bile salts necessary to digest fat, allowing unabsorbed/undigested fat to pass into the colon and come out as greasy stool.4 3 In more serious cases, the impairment to nutrient absorption may lead to vitamin deficiencies — not only of the fat-soluble variety but also of vitamin B12 — and the bacterial overgrowth damages gut lining, which may in turn lead to health issues downstream, such as osteoporosis and/or kidney stones from attendant calcium malabsorption.5

You’ll notice these symptoms are common to other gastrointestinal conditions, so a proper diagnosis should require something like breath testing and/or stool testing.

Causes of SIBO

SIBO may arise when one or more of the following gastrointestinal characteristics weaken:6

Multiple secondary factors increase one’s susceptibility to these causative factors. Age, for example, correlates with slower gut motility and lower gastric acid levels; abdominal surgery and radiation exposure elevate the risk of structural damage; and many health conditions can affect both motility and intestinal structure:6

• Autoimmune diseases such as type 1 diabetes and lupus
• Gastrointestinal disorders such as inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS)
• Other diseases and disorders such as pancreatitis, scleroderma, renal failure, liver cirrhosis, and colon cancer

Types of SIBO

SIBO is categorized according to the main gases produced by the bacterial overgrowth in the small intestine, as measured by a breath test:

What may initially seem counterintuitive — adding microorganisms in a disorder characterized by bacterial overcolonization — might make sense if you change your perspective.

Imagine your small intestine as a home garden, and SIBO as an infestation of aphids. While you could bombard the whole thing with something like a pesticide, which might harm your crops as much as the pests, there’s also a nondestructive method at your disposal: adding ladybugs to the ecosystem. Because a single ladybug can eat up to 5,000 aphids in its lifetime,9 a few dozen or a couple hundred of the spotted lovelies could reasonably control your pest problem and allow your plants to thrive.

With SIBO, it’s roughly the same situation. Similar to how ladybugs compete with aphids, helpful microorganisms in a probiotic supplement can compete with the bad actors in your small intestine and eventually edge them out for nutrients and attachment sites. Potentially, the probiotics may also confer benefits related to bowel function and motility that counter some of SIBO’s ill effects.

The probiotic-only treatment method finds some, albeit low-quality, support in clinical research. For example:

• A 2017 systematic review and meta-analysis reported that probiotics-intervention groups showed a “significantly higher SIBO decontamination rate” compared with control, as well as “significantly reduced” hydrogen concentrations on breath tests and “marked decrease” in abdominal pain scores. Intervention groups did not exhibit improved stool frequency, however, leading the researchers to conclude that probiotics could not play a preventive role, only perhaps an eliminative one.10 The studies included in the review/meta-analysis were highly heterogeneous, using different species, treatment cohorts, and diagnostic methods.
• A systematic review and meta-analysis from 2024 reported a “favorable effect of probiotics in resolving SIBO by hydrogen breath test.” Here, too, the studies were highly heterogeneous, and the researchers noted a “high risk of bias.”11

Since clinical research on the matter is limited, there’s nothing resembling a standard probiotic regimen for treating SIBO. The American Gastroenterological Association doesn’t even mention probiotics in its 2020 best-practice recommendations, instead advising that “management should focus on the identification and correction ... of underlying causes, correction of nutritional deficiencies, and the administration of antibiotics.”12

For most people, then, the place that probiotics hold in their SIBO treatment protocol may be as an adjunct rather than a stand-alone therapy. Especially if antibiotics are part of the treatment, a probiotic supplement may help reduce the risk of developing common antibiotic side effects, such as diarrhea, and perhaps more quickly restore one’s gut microbiome.13

That being said, the efficacy of any therapeutic option may depend on the individual. In some cases, probiotics alone may make a meaningful difference.

Specific probiotic species share certain characteristics that make them more suitable than others for SIBO, and more narrowly, specific strains may be capable of conferring benefits that are particularly helpful for mitigating SIBO’s symptoms.

Below are some species and/or strains that have acquitted themselves fairly well in SIBO-related studies.

Probiotics have a good short-term safety record, broadly speaking. For many people, side effects are limited to temporary gastrointestinal upset — abdominal cramping, nausea, flatulence, soft stools, and the like.18

But because we’re talking about SIBO probiotics, specifically, a minor side effect can compound existing symptoms. Consider, for example, that both SIBO- and probiotic-associated flatulence is a byproduct of bacterial fermentation, so here we have a case of the remedy potentially exacerbating a hallmark symptom, at least for a time. The resulting discomfort may be enough to qualify as a safety concern.

There’s also a rare but serious risk associated with probiotics that contain S. boulardii, which has been linked to a life-threatening infection called Saccharomyces fungemia. In a 2021 report, which examined 43 fungemia cases in Finland between 2009 and 2018, the United States Centers for Disease Control and Prevention reported that “at least 20” of the affected individuals were using S. boulardii probiotics, suggesting a correlation.19 The risk seems to apply largely to the immunocompromised, the critically ill, and people with indwelling catheters, but it’s something that all S. boulardii users should be aware of.

Of final note, be aware that, outside of S. boulardii, immunocompromise or critical illness may contraindicate you for probiotic supplementation in general, as even beneficial bacteria may become opportunistic pathogens under certain conditions.20 It’s risks like these that underscore the importance of consulting a doctor before adding a supplement to your health routine.

SIBO probiotics are principally for people with SIBO. To narrow it down, we’d say they’re best indicated for SIBO patients who:

• Have a clear therapeutic endpoint (e.g., alleviating diarrhea)
• Understand that probiotic therapy has only limited research support for SIBO
• Either accept the risks associated with self-guided probiotic supplementation or want to try probiotics as part of a larger treatment plan, like one that includes antibiotics

These parameters leave us with a large exclusion cohort. Whereas with most other probiotics it’s more or less sensible to just try things out toward a nebulous objective such as “improving gut health,” SIBO probiotics are formulated with too narrow a set of outcomes to accommodate such a laissez-faire attitude. At best, a therapeutic failure would leave the user in the same poor condition as before; at worst, it could leave them with a life-threatening infection (rare) or at least temporarily worsen symptoms (not uncommon).

To prevent disappointment, approach SIBO probiotics with tempered expectations. Remember, SIBO is complex, and something as simple as over-the-counter supplementation may not present a true solution. Your due diligence should therefore include asking your doctor whether one of the probiotics in this guide is a reasonable treatment option for you specifically.

Best single-strain probiotic

Florastor Dual Action Probiotic rests on the strength of one strain that has performed well in research settings: S. boulardii CNCM I-745. In a 2024 randomized, placebo-controlled trial, for instance, it was this strain that led to an 80% SIBO elimination rate in the intervention group, compared with just 23.1% with placebo.15 Some earlier research yielded promising results, too, such as a 2023 pilot study in which the CNCM I-745 group exhibited greater decreases in hydrogen excretion and better improvements in IBS symptoms. The researchers concluded that CNCM I-745, especially when combined with a sensible diet, “reduced bacterial overgrowth and improved digestive symptoms while restoring the intestinal microbiota.”21 Also, keep in mind that S. boulardii is a yeast probiotic species, so it may accompany antibiotic therapy.

The results are encouraging, but should be interpreted with a sober eye. The studies were small, with only 33–54 participants apiece, and in the case of the 2024 trial the participants all had advanced liver disease. So, something like an 80% elimination rate can’t be reasonably extrapolated to the general SIBO public.

Still, CNCM I-745 is currently one of the best-studied probiotic solutions for SIBO, boasting direct supportive clinical research, and Florastor is a reputable brand whose CNCM I-745 has been administered to good effect in clinical gut health studies.22 Together these factors are why we’ve named Florastor Dual Action Probiotic our best single-strain option for SIBO.

Florastor does leave us with a lingering question as to dose, however, as it measures CNCM I-745 quantity in milligrams rather than the standard CFU. Florastor’s reasoning is that S. boulardii is a yeast probiotic, the average size of which is “approximately ten times the size of a single probiotic bacterial cell.” But we can make an educated guess as to Dual Action’s probiotic count based on a 2021 study, which equated 250mg of Florastor to 5 billion CFU.23 That would mean that a two-capsule, 500mg serving of Florastor Dual Action Probiotic contains 10 billion CFU, which is broadly congruent with research on CNCM I-745’s benefits for gut complaints such as diarrhea.24

Pricing and returns

Through the Florastor website, the Dual Action Probiotic is sold in four quantities:

At these price points, Florastor is significantly less cost-effective than our other recommendations, which range as low as $21.99 per bottle or $0.33 per serving.

Yet Florastor is the only brand in this guide that offers free shipping on nonsubscription items at a sub-$100 threshold. In fact, Florastor’s free-shipping threshold is just $24.99, which is a low barrier to cross, and anything above the 20ct option gets you there.

The return window is 30 days. Florastor’s policy isn’t well-delineated, but it leaves the possibility that opened items are eligible for a refund, contingent on approval.

Best multi-strain probiotic

Microbiome Labs RestorFlora combines four probiotic species, each specified down to the strain level and evidentially capable of improving SIBO symptoms:

The sum of it is that the probiotics in Microbiome Labs may not have the same direct SIBO research support as Florastor, but its strains have mostly performed well against gastrointestinal symptoms that are characteristic of the condition.

Pricing and returns

Direct purchases through Microbiome Labs is a pain. First, you have to register an account. Then you have to get a medical practitioner’s approval to buy a product — odd, considering that RestorFlora is not a prescription medication.

To avoid all that, we recommend buying through a third party, such as Amazon, where a one-time purchase is $45.77 and a subscription costs $41.19. The one-timer is equal to the price point listed on the Microbiome Labs website, and the subscription cost is roughly $2.00 lower.

A single bottle contains 60 servings, or two months’ worth, so the per-serving cost equals no more than $0.76, which isn’t bad.

With Amazon, though, you probably can’t get a refund on an opened order, as the e-commerce conglomerate typically doesn’t allow returns of supplements. Microbiome Labs does have a return policy, with a 45-day window, but it involves a phone call to the company and explicit authorization of a return — similar to BioGaia. Only NOW’s direct return policy is worse, as it doesn’t allow returns on opened items at all.

Best for methane SIBO

BioGaia Gastrus Probiotic Chewables comprises two Limosilactobacillus reuteri strains with decent, albeit limited, supportive research behind them:

The BioGaia chewables are pretty tasty, by the way. Somehow they remind us of Fruity Pebbles on the front end, and Smarties on the back. A palatable flavor isn’t something one normally expects from a probiotic, so we were pleasantly surprised.

Pricing and returns

BioGaia Gastrus Probiotic Chewables sell at multiple price points, one of which is a two-pack bulk:

Buying one bottle as a one-time purchase isn’t as bad as Florastor, but it’s significantly costlier than Microbiome and NOW. The one-bottle subscription option is better, but also not as cost-effective as Microbiome or NOW. Only at the bulk level does the per-serving cost dip below that of Microbiome.

Subscriptions ship free, but all other orders get $6.95 tacked on to the bill.

The return policy is almost identical to that of Microbiome’s, except with a shorter, 30-day window. That is, you have 30 days to call (not email, but call) BioGaia to request approval on a return/refund.

Lowest up-front cost

NOW Foods Saccharomyces Boulardii contains 10 billion CFU of the eponymous probiotic yeast species, a clinically supported quantity.24 It doesn’t identify the strain of S. boulardii it uses — an obvious weakness, as probiotic benefits are strain-specific — but it can still do some good, seeing as S. boulardii in general has yielded gut health improvements in clinical research. Indeed, a 2015 systematic review notes that the S. boulardii family has reduced the risk of antibiotic-associated diarrhea in adults from 20.9% to 8.8%, a significant change.32 So, while we wish NOW Foods had used CNCM I-745 like Florastor, or even CNCM I-1079 like Microbiome Labs, its formulation as it stands still may be capable of improving SIBO symptoms.

Plus, with any NOW Foods supplement, you get a strong pedigree of official assurances. The Saccharomyces Boulardii supplement, in particular, boasts six certifications —

• Halal
• Kosher
• Vegan
• Keto-Friendly
• Non-GMO
• Intertek GMP

— so you can be confident you’re getting a product that is suitable for your dietary restrictions and that has been made under strict manufacturing practices.

You do, however, need to refrigerate the bottle after opening, which no other product in this guide requires.

Pricing and returns

NOW Foods Saccharomyces Boulardii is the most affordable SIBO probiotic among our recommendations. It’s sold in two quantities:

• 60ct (30 servings): $21.99
• 120ct (60 servings): $39.99

The 60ct bottle costs $0.73 per serving, which is $0.03 lower than that of Microbiome Labs and $0.03 higher than that of BioGaia at the bulk level. But with the 120ct bottle, the per-serving cost drops to $0.67, which handily beats any of our other recommendations.

No direct subscriptions, though, and no refunds on opened items. So the value benefit relates only to the up-front and per-serving costs, not to additional savings or purchase protection.

The best alternatives to SIBO probiotics — rather, what should be your first-line interventions — are prescription antibiotics and temporary dietary changes.

Antibiotics are the most established treatment approach. We reiterate that the American Gastroenterological Association advises that SIBO management ought to prioritize antibiotics alongside the correction of underlying causes.12 Although recurrence may still be possible, this approach presents the best odds of eliminating SIBO. If you’re using probiotics, they ought to play an adjunctive role.

As for dietary changes, you’ll want to follow what’s called an elemental diet, which replaces ordinary food with nutritionally complete substitutes whose nutrients are readily absorbed by the body, limiting the quantity of residues that small intestinal microbes can feed on. In a 2025 trial, this diet led to normalized breath tests in 73% of subjects with SIBO, as well as adequate symptom relief in 83%.33

These interventions are clinician-led. You might try a self-directed low-FODMAP diet instead, but the prognosis likely wouldn’t be as good compared with an elemental diet, prescription antibiotics, and possibly adjunctive probiotics.