SIBO, Probiotics, and Your Gut Health: A Long-Term Strategy


You may have read internet advice that suggests you should never take probiotics if you have small intestinal bacterial overgrowth (SIBO). Since the condition is caused by an excess of bacteria (including beneficial bacteria) in the small intestine, why would you add more?

However, if you follow that advice, you’d be missing out on a research-backed, effective treatment.

Let’s discuss how following the research can enable you to overcome SIBO by using probiotics and other safe, effective therapies.

SIBO probiotics: Depiction of probiotics under microscope

Treating SIBO With Probiotics

Even though it may seem counter-intuitive, research CLEARLY shows that probiotics can be very effective for treating SIBO, improving both symptoms and lab values. [1 Trusted SourcePubMedGo to source]

  • One SIBO-probiotics study found probiotics to be more effective than Metronidazole, an antibiotic treatment for SIBO. [2 Trusted SourcePubMedGo to source]
  • A meta-analysis summarizing 18 clinical trials concluded that probiotics are an effective treatment for SIBO. [3 Trusted SourcePubMedGo to source] Specifically, probiotics reduce bacterial overgrowth and hydrogen concentrations, and improve symptoms, including abdominal pain.
  • Another study found that probiotics work much better in patients with both IBS and SIBO, as compared to those who have IBS without SIBO. [4 Trusted SourcePubMedGo to source]

The SIBO-IBS Link

SIBO probiotics: The SIBO-IBS link

Before we dive into other research-backed treatments for SIBO, it’s important to clarify the link between SIBO and irritable bowel syndrome (IBS).

SIBO is not a “condition” in itself. It is, in fact, a lab finding, usually based on a glucose or lactulose breath test. It’s possible to test positive for SIBO and be perfectly healthy, without symptoms.

IBS is not exactly a “condition” either, it is a set of digestive symptoms that include bloating, abdominal pain, diarrhea and/or constipation. There is no test for IBS. Patients who test positive for SIBO may have IBS symptoms.

SIBO is a potential cause of IBS. However, it is not the only possible cause. A recent meta-analysis (highest quality research) reviewed 50 clinical studies and found that:

SIBO falls under a broader umbrella term of digestive tract dysbiosis. Dysbiosis, simply stated, means an imbalance of bacteria, fungus, and other organisms of the digestive system. Most treatments that work for dysbiosis also work for SIBO.

Probiotics and Your SIBO Treatment Plan

SIBO probiotics: SIBO treatment plan

When it comes to treatment of SIBO, quick fixes don’t always work. Long-term success is possible, however, through a combination of treatments that address intestinal dysbiosis and improve digestive health. This may include probiotics, [7 Trusted SourcePubMedGo to source] diet, [8 Trusted SourcePubMedGo to source] fasting, [9 Trusted SourcePubMedGo to source] digestive supports, [10 Trusted SourcePubMedGo to source] and herbal antimicrobials. [11] All of these treatments are supported by research.

Every SIBO patient has a unique intestinal microbiome and the best combination of SIBO treatments for one may not be the best for another. What will work for you can only be learned through a process of personal experimentation.

Probiotic supplements are an excellent place to start in your personalized SIBO treatment plan. They are simple to use, safe over the long term, [12, 13 Trusted SourcePubMedGo to source] and backed by research. In fact, while the research described above supports using probiotics for SIBO, there’s even more research to support using probiotics for IBS symptoms. [14 Trusted SourcePubMedGo to source, 15 Trusted SourcePubMedGo to source, 16 Trusted SourcePubMedGo to source, 17 Trusted SourcePubMedGo to source]

As I discuss more fully in my book Healthy Gut, Healthy You, probiotics are a very important foundational strategy for treating IBS and other digestive problems.

SIBO Probiotics Tips

Though there are hundreds of probiotic supplements on the market, most probiotics fall into one of these three categories:

IBS research has concluded that multispecies probiotics work better for IBS. [18 Trusted SourcePubMedGo to source, 19 Trusted SourcePubMedGo to source]  Using one type of probiotic is good, but using all three different probiotics together allows them to work synergistically to improve your gut health.

The three types of probiotics work together like the legs of a three-legged stool. If the stool only has one or two legs, it’s likely to be unstable. With three legs, the stool is able to stay upright.

SIBO probiotics: Shows how probiotics work together for gut health

Choose high quality probiotic supplements with a high count of CFU (colony forming units). Keep in mind that probiotic manufacturing is not well-regulated and some labels’ claims do not stand up to scrutiny. [20, 21, 22]. Look for:

  • A clearly stated list of probiotic species
  • A clearly stated number of colony-forming units (CFUs) in the billions
  • A manufacture date and/or expiration date
  • Labeled free of common allergens and other substances you may wish to avoid (e.g. gluten-free, non-GMO, vegan)
  • Good Manufacturing Practices (GMP) certification
  • Lab-verified for probiotic species and potency by third-party analysis (independent lab testing)

Other SIBO Treatments

Here are some other treatments that you may want to try. Go slowly, try them one at a time, and assess their impact on your SIBO symptoms. If after a few weeks, you don’t see a difference in your symptoms, discontinue that treatment. How your body responds is more important than breath test results.

Low FODMAP Diet

SIBO probiotics: foods included in low-FODMAP diet

Diets that restrict bacteria-feeding carbs have been shown to improve SIBO and IBS symptoms. [23 Trusted SourcePubMedGo to source, 24 Trusted SourcePubMedGo to source, 25 Trusted SourcePubMedGo to source, 26 Trusted SourcePubMedGo to source] These are known as low FODMAP diets.

One review of 10 clinical trials found that the low FODMAP diet led to clinical response in 50%–80% of patients with IBS symptoms. [27 Trusted SourcePubMedGo to source] This review also found that the low FODMAP diet results in profound changes in the microbiota and in overall gut health. It reduces leaky gut, inflammation and histamine (a marker of an overzealous immune system).

Digestive Supports

Adequate stomach acid (HCI) production is crucial for the digestive process and helps to keep bad bacteria in check. Some people don’t produce enough stomach acid for proper digestion.

Research into the long-term effects of proton pump inhibitors (drugs that lower stomach acid) gives us some insights into the risks of low HCI production. [28 Trusted SourcePubMedGo to source, 29 Trusted SourcePubMedGo to source, 30 Trusted SourcePubMedGo to source] Inadequate stomach acid is one of the risk factors for SIBOand fungal infections in the small intestine (SIFO).

Digestive enzymes are also crucial for the digestive process. Anyone who eats a standard American diet, may not be getting enough digestive enzymes from their diet.

While there are no clinical studies for digestive enzymes and SIBO, we can look at the research more broadly and see that digestive enzymes may contribute to the overall goal of improving digestive health. [31, 32 Trusted SourcePubMedGo to source]

Supplemental HCI and digestive enzymes are available separately or in combination formulas.

Prokinetics are agents that support healthy motility in your stomach and intestines. Motility means that food moves through your intestinal tract at the right pace. Motility keeps your intestinal ecosystem in balance, much like flowing water of a river or stream. Stagnant pond water fosters bacterial growth and the same is true of food in your digestive system.

Antimicrobial Therapy

A standard SIBO treatment is antibiotic therapy with Rifaximin, which reduces unwanted gut bacteria in both the small and large intestine. Research shows that this approach eliminates SIBO for 67% of patients. [33 Trusted SourcePubMedGo to source]

Herbal antimicrobials work in the same way as Rifaximin and are more commonly used in functional medicine. There are fewer studies for herbal antimicrobials, but they have been shown effective in IBS and SIBO. [34 Trusted SourcePubMedGo to source, 35 Trusted SourcePubMedGo to source]

Many of these herbal medicines also have beneficial side effects. They are anti-inflammatory and perhaps even antidepressant. [36, 37] Herbals may also combat other bacterial and fungal imbalances that might not have been detected through testing, such as candida overgrowth. [38 Trusted SourcePubMedGo to source] Many herbal medicines act against bacteria, fungi, and protozoa while antibiotics mostly work against bacteria.

Anecdotal evidence suggests that, long-term, some patients relapse after antimicrobial and antibiotic therapy. For some SIBO patients, there may be underlying causes that allow unwanted gut flora to repopulate the small bowel.

This is where an ongoing strategy for digestive health can provide better long-term results when compared to one single, short-term treatment. A personalized approach that may include probiotics, dietary changes, digestive aids, and antimicrobial treatment may work better in the long run for keeping gastrointestinal symptoms in check.

Elemental Diet

SIBO probiotics: elemental shake in glass with glass dish of powder

Elemental diets were developed as a medical food to treat patients with severe digestive issues. This dietary product is essentially a fast for your gut microbes. Drinking elemental shakes for 2-3 weeks, with no other sources of calories, often achieves results when other gut therapies have failed.

Research into elemental diets has focused on inflammatory bowel disease, [39 Trusted SourcePubMedGo to source, 40 Trusted SourcePubMedGo to source, 41 Trusted SourcePubMedGo to source, 42 Trusted SourcePubMedGo to source, 43 Trusted SourcePubMedGo to source, 44 Trusted SourcePubMedGo to source, 45 Trusted SourcePubMedGo to source, 46 Trusted SourcePubMedGo to source, 47 Trusted SourcePubMedGo to source, 48 Trusted SourcePubMedGo to source, 49 Trusted SourcePubMedGo to source]. We don’t yet have a lot of research into elemental diets and SIBO. However, one exciting study saw lactulose breath tests normalize in 80% of SIBO patients after two weeks on the elemental diet. [50 Trusted SourcePubMedGo to source] Sixty-five percent of patients in the same study saw an improvement in their IBS symptoms.

Elemental meal replacement shakes can be used in flexible ways to manage SIBO symptoms. Even a “half” elemental diet (up to 50% of daily calories from elemental shakes) reduces gut symptoms and flares. [51 Trusted SourcePubMedGo to source] Elemental meal replacement shakes can be an effective part of a long-term SIBO management strategy.

The Extra Benefits of Treating SIBO

If you have been struggling with IBS symptoms, getting them under control is a big win. Even better, by treating digestive tract dysbiosis, including SIBO, you may experience beneficial effects on other health conditions.

Research shows that successful SIBO treatments can also lead to improvements in:

SIBO is also associated with a number of other conditions, including: hypothyroid, [63] coronary artery disease, [64 Trusted SourcePubMedGo to source] diabetes, [65 Trusted SourcePubMedGo to source] chronic kidney disease, [66 Trusted SourcePubMedGo to source] chronic pancreatitis [67 Trusted SourcePubMedGo to source] and Parkinson’s disease. [68 Trusted SourcePubMedGo to source]

We don’t yet have research to show if SIBO treatments can help to resolve these conditions.

Probiotics Are Effective for SIBO

Be wary of internet advice that suggests probiotics will make SIBO worse. This is one area where, sadly, opinion has drifted away from science. Probiotics are an effective treatment for SIBO and can be used alone or in combination with a number of other research-backed treatments.

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SIBO patients may benefit most from a long-term strategy to improve overall digestive health rather than short-term, SIBO-focused treatments.This approach has benefits beyond treating SIBO and can help resolve digestive symptoms, non-digestive symptoms, and chronic inflammatory conditions.

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