Small intestine bacterial overgrowth (SIBO) causes annoying bloating, constipation, diarrhea (or both), and an inability to digest certain carbohydrates. The worst part about SIBO is the bloating: I’ll often hear my clients tell me that by the end of the day, they look 6 months pregnant.

When addressing any digestive issue, you may assume probiotic supplements will be beneficial. That can be true in some cases, but treating SIBO isn’t a one size fits all approach. While some people benefit from probiotics during their SIBO treatment, others may feel worse on a probiotic. To complicate matters, there are certain probiotics we know to be more effective, and others that should be avoided when treating SIBO.

Should you take a probiotic if you have SIBO? What are the best probiotics for SIBO?

What is SIBO?

SIBO is an overgrowth of bacteria in the small intestine. The small intestine is fairly sterile and shouldn’t really be home to much of the bacteria present in the large intestine, so when bacteria take root in the small intestine, symptoms such as pain, bloating, belching, abdominal distention, reflux, constipation and/or diarrhea result as the bacteria ferment the carbohydrate fibers you eat.

These aren’t necessarily pathogenic bacteria; they’re just bacteria trapped in the wrong place. The crux of digestion occurs in the small intestine, so when something is in there that shouldn’t be in there, digestion suffers. In the case of SIBO, when you eat certain fruits, vegetables, grains, nuts, legumes, or some dairy products (high FODMAP foods), the bacteria ferment the starches in these foods and release hydrogen and/or methane gases that cause the bloating and the altered transit time many SIBO sufferers experience.

The main cause of SIBO that I see is food poisoning that damages or destroys nerve cells in the intestinal tract which causes impaired gut motility. Hypothyroid, low stomach acid, structural issues (like adhesions from trauma or surgery), antibiotic use, steroid drugs, and prolonged use of antacids (PPIs) are also causes. Read my post on SIBO here for more details. Note that if you have been diagnosed with IBS, you should be tested for SIBO, as there is a big correlation between IBS and SIBO.

How is SIBO Treated?

Determine if you have SIBO from a breath test, which you can order here. (the 3 hour lactulose is the best option). The test will let you know if you have hydrogen dominant SIBO or methanogen overgrowth (IMO). You need to know this info to design the best treatment. SIBO treatment is a combo of diet, herbs, and healing leaky gut. SIBO damages the small intestine, so the gut healing piece once you’ve eradicated it is the most important step.

So, what about probiotics?

Earlier I mentioned that the small intestine is relatively sterile and isn’t home to much bacteria. Your large intestine (colon) is where the millions of bacteria in your gut live. These bacteria ferment and digest fiber for you. So it might seem odd to take probiotics for a condition in the small intestine where bacteria shouldn’t colonize. But the health of the large intestine affects the small intestine, and there are some probiotic strains we have found beneficial for SIBO treatment. Some studies have also shown that probiotics can support SIBO treatment and really improve patient outcomes. (source)

In fact, in patients suffering from SIBO, the treatment efficacy of probiotics was remarkable. The SIBO decontamination rate achieved with probiotics alone was 53.2%, which was comparable to that observed in a meta analysis on antibiotics (51.1%). (source)

Best Probiotics for SIBO

Probiotic supplements can be very beneficial for people with digestive issues. Probiotics deliver live microorganisms to the large intestine, and there they help break down and ferment the food you eat. Probiotic supplements don’t stick around and colonize in the gut, but they can help improve symptoms and the health of the gut while you take them. Ultimately you need a healthy gut lining and a diet rich in prebiotics (from fiber) to form robust colonies of probiotics that stick around in the gut and make you healthier, but most people with SIBO cannot tolerate fiber-rich foods.

If you have SIBO, probiotics can ease constipation, normalize bowel function if you have diarrhea, and improve mucosal barrier function (fancy way of saying promote gut healing).

Note that probiotics may not be right for everyone who has SIBO. I have seen some SIBO people feel much worse taking a probiotic (bloating and feeling worse on a traditional probiotic is a symptom of SIBO), while others improve quite a bit.

Inability to tolerate probiotics if you have SIBO is usually caused by two issues: histamine intolerance and supplement fillers. People who have SIBO are more likely to be histamine intolerant, and some probiotics will worsen bloating and other symptoms consistent with histamine intolerance. Secondly, some probiotic brands contain fillers like inulin, maltodextrin, and/or tapioca starch, and that will bloat you if you have SIBO.

Typically the strains I mention below work best for the majority, but it’s not always the case. SIBO is a very complex digestive condition, and it helps to work with an experienced practitioner rather than going it alone.

Saccharomyces boulardii gets top billing. It’s not actually a probiotic; it’s a strain of yeast that acts like a probiotic in the gut. It’s very helpful for diarrhea, and I always recommend it for hydrogen dominant SIBO that often causes loose stool. It’s also great for traveler’s diarrhea and candida.

Many people tolerate sacc b well. It has anti-inflammatory effects in the gut and can inactivate pathogenic toxins. (source). It may also offset digestive side effects common when you take antibiotics. In fact I always recommend taking sacc b if you have to take antibiotics (read more on that here). I recommend this sacc b, and the dose is usually 2 per day. If you choose another sacc b, make SURE you get one without FOS (fructooligosaccharides) or fillers.

Bacillus species soil-based probiotics get second prize and are all the rage right now. They’re called spore or soil-based probiotics because  they’re found everywhere in soil and water, and they often spend part of their life cycle in the dormant “spore” state. We used to be exposed to these bacteria frequently when we were a more agrarian society, but these days since we spend so much time indoors in sterile environments, we lack exposure to soil-based organisms.

Soil-based probiotics are great for reducing inflammation and healing the leaky gut that often accompanies SIBO. They also improve diarrhea, abdominal pain, bloating, and stool consistency in IBS patients (remember there’s a correlation between SIBO & IBS). (source)

You’ll most often see bacillus coagulans and bacillus subtilis soil-based probiotics. MegaSpore Is a great one (check it out here). The dose is 2 per day, but you may need to work up to this full dose very slowly. In my experience, the more damaged your gut lining, the more likely you are to have a reaction. Introducing the probiotic very slowly (I have people break open the capsule) so your gut and immune system get used to it can mitigate adverse reactions. This one is also good.

Bifidobacterium: smaller studies have shown that bifido-lactobacillus probiotic combos are effective against SIBO. I have to say that anecdotally, I have not seen this to be true. That means that in my own clinical experience, most SIBO (not all) people do not do well on traditional lactobacillus strains. Again, this is my own opinion. But I have seen good results with bidifo only strains, or this particular bifido sacc b combo is great.

Lactobacillus reuteri has the capacity to produce an antimicrobial compound called reuterin. Reuterin is active against methanogens and also the main bugs that accompany in SIBO, like E. coli and Klebsiella and streptococci. In studies it’s been shown to reduce methane gas and improve constipation that accompanies methanogen overgrowth.  (source) This product is a good source. It’s labeled as a baby formula, but the dose for adults is 10 drops before bed.

Bifidobacterium bifidum and longum have been studied particularly for SIBO. Interestingly, B. infantis worsened methanogen overgrowth in this small study.

Who Should Not Use Probiotics?

First off, if you have SIBO avoid probiotics with prebiotics which can feed SIBO bacteria and worsen bloating. Also, avoid probiotics with additives that can also worsen your symptoms.

If you know that you are histamine intolerant and you have SIBO, tread lightly. There are certain probiotic strains you’ll definitely want to avoid because they cause histamine release in the gut. These species may increase your body’s natural histamine production:

• Lactobacillus casei
• Lactobacillus Bulgaricus
• Streptococcus thermophilus
• Lactobacillus delbrueckii
• Lactobacillus helveticus

Don’t take probiotics if they cause unpleasant lingering side effects, especially a worsening in bloating. Sometimes MegaSpore can cause a change in stool or slight cramping, but that should subside. Typically it means you should cut down on the dose and work back up slowly.

Conclusion: The Two Best Probiotics for SIBO

Your microbiome is as unique as your own fingerprint, so depending on what species (beneficial and pathogenic) you harbor in your gut and in what amounts, the same probiotic could affect you and someone else differently.

My personal top recommendation for SIBO people is saccharomyces boulardii. I recommend this one, 2 daily. I also highly recommend this probiotic, GI Distress, which is a sacc b bifido combination. It’s  great for IBS, IBD, Crohn’s, colitis, C. difficile infection, SIBO, and histamine intolerance. MegaSpore is also a great soil-based probiotic that has been used by many SIBO sufferers with great results.

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Mary Vance (Certified Nutrition Consultant)

Mary Vance is a Certified Nutrition Consultant and author specializing in digestive health. She combines a science-based approach with natural therapies to rebalance the body. In addition to her 1:1 coaching, she offers courses to help you heal your gut and improve your health. Mary lives in San Francisco and Lake Tahoe in Northern California. Read more about her coaching practice here and her background here.