SIBO Probiotics: The Best Brands & How to Use Them During or After Treatment

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Probiotics get a bad rap in the SIBO community.

The common assumption is that adding more bacteria to the mix wouldn’t be helpful for someone with SIBO. Bad motility might mean those bugs hang out too long in the small intestine and potentially join the ranks.

The reality is a lot more nuanced.

Over the last 5 years, probiotic supplements have sky-rocketed into a highly lucrative global industry. Many brands promise to deliver billions of organisms to your colon, along with any number of health benefits from weight loss to reduced risk of heart disease. However, one of the general misconceptions about probiotics is that these bottled bugs join your existing bacteria and take up permanent residence in the gut.

Rather, probiotic bacteria are transient visitors that allow the immune system to fine-tune its response to more dangerous microbes.

In a roundabout way, this does encourage more beneficial bugs to thrive and increase in population. As I talk about in my book, you cannot have a happy gut without a calm, responsible immune system. But more notably, different probiotic strains have specific actions as they pass through your system.

If you are going to use probiotics for SIBO treatment, you have to have some degree of savvy, otherwise you do risk potentially aggravating your overgrowth.

Today we are going to do a deep dive into the best types of SIBO probiotics, when to use them, and (perhaps more importantly) how they can work together with prebiotics to heal your gut during or after SIBO treatment.

Read on for all my tips and tricks, and if you want even more of a breakdown on SIBO supplements, make sure to pick up a copy of SIBO Made Simple.

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Some probiotics are antimicrobial agents. Others can improve gut transit time and stimulate the migrating motor complex, much like a prokinetic.

The key, especially when it comes to treating SIBO with probiotics, is to drill down and match the appropriate bacterial strains with the desired action.

This was a big lesson from my podcast conversation with Dr. Jason Hawrelak, who did his PhD on the role of dysbiosis in irritable bowel syndrome and is now a highly sought-after probiotic researcher, educator and clinician.

“If we’re talking about reducing the numbers of excessive microbes, we’re after probiotic agents that have demonstrated antimicrobial activity against the microbes that are most commonly present in SIBO,” he said.

One particular strain Hawrelak uses in his practice is the DSM17938 strain of Lactobacillus reuteri, which was recently studied to see whether it could prevent SIBO development in patients taking proton pump inhibitors (PPI’s).

Use of PPI’s puts you at a significant risk of SIBO—1.71 times more likely than the average person according to a 2017 meta-analysis published in the Journal of Gastroenterology. The theory is, when your stomach acid is being suppressed, you miss a vital step in the digestive process that reduces the chances of bacteria making their way to your small intestine. In this study, 56% of the children taking PPI’s developed SIBO, while only 6% of those taking PPI’s along with this particular strain of Lactobacillus reuteri developed SIBO.

The Best Probiotic for SIBO and how to use during or after treatment for gut healing

What makes this probiotic strain so effective is its capacity to produce an antimicrobial compound that’s incredibly effective against E. coli, Klebsiella, and other bugs commonly found in SIBO. In other words, the probiotic seems to effectively do stomach acid’s job of killing off unwanted critters entering the body in the absence of it.

For those who are prone to food poisoning or have underlying causes that might put them in a similar risk group, certain probiotic strains could be a game changer for preventing chronic SIBO. Similarly, other probiotic strains that increase motility could provide an essential action for those who tend towards constipation.

Unfortunately, this is a complicated equation and most practitioners are not well-versed enough in the particulars of probiotics to be able to lean on them as a de facto prescription. And most people don’t work with practitioners at all when it comes to probiotics, which some practitioners, like Hawrelak, say can cause some sufferers to run into trouble.

Still, meta-analyses of research over the last fifty years using probiotics in the treatment of IBS show mostly positive outcomes for shifting symptoms. If SIBO is indeed the underlying cause of the majority of IBS cases, it seems silly to discount probiotics as a possible avenue for treatment, managing GI symptoms, or prevention.

That said, most SIBO-specific practitioners don’t recommend dabbling in probiotics until after a round of treatment (more on this here) to rebuild the bacterial integrity of the large intestine. Since everyone’s microbiota is more unique than a fingerprint, it may take some trial and error to find the combination of probiotics that agrees with you.


Most probiotics fit within one of the three groupings below, and if you find you get a negative reaction it is likely due to the type (soil versus Lacto-bifido) rather than the specific brand.

It’s easiest to start with one of the below categories and layer from there to avoid an adverse reaction that you can’t get to the bottom of. Those who tolerate a variety can work their way up to all three.

Lactobacillus and bifidobacterium blends: Both Lactobacillus and Bifidobacterium strains are widely studied for their treatment of various infectious and inflammatory conditions. Most commercial probiotics on the market offer combinations of these strains. However, when bacteria are present in the small intestine, they are often one of these species, which is why some practitioners avoid using lacto-bifido blend probiotics during treatment and often turn to one of the two below afterwards.

Soil-based probiotics: Spore-forming microorganisms that populate our soil used to have a much wider presence in our own digestive system. Since our food supply (and lives) have become increasingly sanitized and devoid of natural probiotic power, supplementing with these organisms becomes an even more necessary pursuit. Soil-based probiotics are incredibly sturdy and able to survive a trip through your stomach acid. They are also heat-resistant, so don’t need refrigeration. This is particularly convenient for travel and preventing food poisoning on the road.

Saccharomyces boulardii: This beneficial yeast is an-around powerhouse for IBS, immune deficiency, healing leaky gut and traveler’s diarrhea. Even those with candida or yeast overgrowth need not fear it. It’s also been specifically studied and seen to decrease hydrogen gas in pediatric SIBO sufferers. If either of the two other groups of probiotics don’t agree with you, s. boulardii is worth a try.

It is also a commonly used probiotic for travelers’ diarrhea, and has also racked up compelling evidence for its capability to preserve and restore intestinal barrier function. Even practitioners who are wary to advise probiotic use during SIBO treatment sometimes recommend taking S. boulardii since it can maintain gut balance but doesn’t run the risk of overgrowing in the small bowel.


Functional Medicine Formulations Soil-Based Probiotic –  I am a big fan of Dr. Michael Ruscio’s wisdom around probiotics and his formulas have worked great for me and many others. This is his soil-based formula, but there are also probiotics that fall into the other buckets in his shop.

Microbiome Labs Megaspore Spore-based Probiotic – This is a very popular soil-based probiotic for SIBO that many doctors recommend. It was one of the first ones I tried after treatment to get my gut on track. Soil-based probiotics are fine at room temp, so they are also a great option for travel.

Biogaia Gastrus Chewable Tablets (Lacto-Bifido Blend) – This is the one brand available in the US that is specifically formulated for motility with the correct strain of Lactobacillus for this action. They are chewables and also make formulations for children.

Functional Medicine Formulations Lacto-Bifido Probiotic Blend – Again, this is Dr. Ruscio’s blend for the lacto-bifido bucket of probiotic. The majority of store bought probiotics fall in this category, but I recommend buying from someone who is savvy to SIBO.

Pure Encapsulations – Saccharomyces Boulardii: I am not very brand loyal to saccharomyces – some people swear by the more generic Florastor. But for best results, you want to look for a bottle in the refrigerated section and go with brands that have live cultures and tell you to keep cool.


One of the resounding pieces of wisdom on gut health that I have come across is that probiotics can only do so much if your diet isn’t laying the necessary groundwork. A helpful analogy is likening probiotics to expensive fertilizer. It’s not going to do your garden any good if you don’t remember to water the plants.

Prebiotics are the water in this scenario and thought to be the most effective food for your gut garden. These selectively fermented fibers encourage the growth of beneficial bacteria (the flowers, if you will) in your large intestines, which can then suppress the expansion of more inflammatory species (the weeds).

The prebiotic that seems to have more beneficial effects for SIBO sufferers than not is partially hydrolyzed guar gum (PHGG). Dr. Hawrelak did a systematic review of all the studies that looked at the use of PHGG in patients with IBS. The analysis showed an overall reduction in symptoms, including bloating, diarrhea, and constipation. It was clear that the prebiotic fiber itself dramatically improved quality of life by shifting the underlying ecosystem of the gut.

For SIBO patients in particular, a compelling study was done that compared the efficacy of rifaximin in eradicating SIBO when PHGG was added to the antibiotic dose. While the rifaximin alone cleared the overgrowth in 62 percent of one group, it was 87% percent effective in the group taking both the rifaximin and the PHGG.

One of the reasons why PHGG works so well for SIBO sufferers is that it is a food source primarily for butyrate-producing bacteria. Butyrate can inhibit the growth of the main organism that’s responsible for methane overproduction. More butyrate-producing bacteria can also improve hypersensitivity in the colon, paving the way for a higher tolerance of all gas-producing prebiotic foods.

In his practice, Dr. Hawrelak has seen PHGG be a successful edition to treatment for both hydrogen and methane-dominant SIBO. And while there is a small subset of people who might not react well to the prebiotic fiber, he’s found it’s tolerated by most of his SIBO patients.The Best Probiotic for SIBO and how to use during or after treatment for gut healing

PHGG is a low risk, high reward supplement. Across the landscape of gut science, there’s a lot of evidence for using prebiotics to increase populations of anti-inflammatory gut healing species. Nothing comes close in the probiotic realm. PHGG is a fairly user-friendly way to experiment as a layman without too many adverse effects, and might be both a boon to your doctor’s treatment plan or your “maintenance” period afterwards. Make sure what you buy is partially hydrolyzed and not just plain guar gum as it is a totally different product.

Not sure you have SIBO? Try a probiotic first. Many people skip the breath test and jump right into a SIBO kill protocol. But just because your IBS symptoms might sound like SIBO, doesn’t mean you have SIBO. Before you start killing off beneficial gut flora, it might be worth trying one or more types of probiotics above. If they make you worse, that could mean SIBO is likely. If they make you better, then you’ve just saved yourself a lot of time and money, and your good bacteria from unnecessary destruction.

Space out probiotics from herbal antimicrobials. Dr. Hawrelak often uses probiotics in tandem with herbal treatments, making sure to space the doses a few hours apart from one another. For example, probiotics can be taken at lunch and before bed time, while herbal antimicrobials are consumed at breakfast and dinner. Again, he is using highly specific strains, not your average over the counter probiotic. If you do go the route of taking probiotics in tandem with treatment, make sure you work with a practitioner who has done their homework.

Probiotic effects are fleeting. The most important thing to keep in mind with probiotics is that their effects are short-lived. They’re not permanent residents. If you begin taking a probiotic strain to help improve motility or constipation, when you stop taking it, you stop getting that benefit.

Give yourself a waiting period after antimicrobials. The most common application of probiotics is after antibiotic or antimicrobial treatment. A recent study that wasn’t specific to SIBO suggests that probiotic usage is most beneficial if you wait 4 weeks after antibiotics to begin the re-seeding process. For SIBO people, this waiting period might also give you a chance to re-test and establish the outcome before proceeding down the probiotics path.


What questions do you have about using SIBO probiotics for treatment or healing the gut afterwards?

I would love to hear more from you in the comments.

For more information on any SIBO subject, check out the book SIBO Made Simple

The Best Probiotic for SIBO and how to use during or after treatment for gut healing


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