How to Use SIBO Probiotics to Personalize Your Treatment Plan

SIBO probiotics: SIBO bacteria

A quick Internet search may lead you to believe that treating SIBO with probiotics won’t work. After all, it may seem counterintuitive to add bacteria when you have a condition caused by bacterial overgrowth in the small intestine.

However, this advice completely overlooks the body of research evidence that plainly demonstrates probiotics can help to treat small intestinal bacterial overgrowth (SIBO) [1]. 

In this article, we’ll take a closer look at the symptoms SIBO probiotics may help relieve, how to find a quality probiotic supplement, and strategies for supporting a healthy microbiota.

What Is Small Intestinal Bacterial Overgrowth (SIBO)?

SIBO is not a “disease” in itself. SIBO is a lab finding based on a breath test (lactulose or glucose). A positive SIBO test means you have too much bacteria in your small intestine. 

SIBO can be categorized as digestive tract dysbiosis. When there is an imbalance between good and bad bacteria or fungus in the digestive system (stomach, large intestine, or small intestine), dysbiosis occurs. 


SIBO probiotics: the SIBO-IBS link

There is a significant overlap between SIBO and IBS, and patients with SIBO often have IBS symptoms. As previously mentioned, SIBO is not a disease or condition — it is a lab finding. IBS (irritable bowel syndrome) is not a disease either. Instead, IBS is a set of symptoms that includes bloating, abdominal pain, diarrhea, or constipation.

IBS is often diagnosed when other disorders are ruled out (celiac disease, Crohn’s disease, inflammatory bowel disease (IBD), and colon cancer). To diagnose IBS, a patient must report altered bowel habits (diarrhea or constipation) and abdominal pain. 

Notable research tells us that SIBO could cause IBS. However, it is not the only potential cause. 

A meta-analysis reviewed 50 clinical studies, which showed:

  • Over one-third of IBS patients tested positive for SIBO [1].
  • Patients with IBS were nearly five times more likely to test positive for SIBO compared to healthy controls, suggesting a high prevalence of SIBO in IBS patients [1].

Research on Treating SIBO With Probiotics

Though some practitioners will warn against using probiotics when you have SIBO, research demonstrates otherwise. In a systematic review and meta-analysis of 18 clinical trials (this is the highest quality of research evidence), probiotics were found to be effective for decontaminating SIBO, reducing hydrogen and methane concentrations, and reducing abdominal pain [2]. 

Other studies have demonstrated equally impressive results:

  • One SIBO probiotics study demonstrated probiotics could be more effective than Metronidazole, an antibiotic therapy for SIBO [3].
  • An additional study found that probiotics are more effective in patients with SIBO and IBS than those who have IBS without SIBO [4].

SIBO Treatment Benefits

SIBO probiotics: SIBO symptoms

SIBO patients may suffer from a surprisingly long list of digestive and non-digestive symptoms. A lot of people don’t know that fatigue, poor mood, brain fog and other non-digestive symptoms may be related to SIBO. Successfully treating SIBO can help to reduce these symptoms. 

A number of health conditions have been linked to SIBO, including rosacea, celiac disease, rheumatoid arthritis, depression, and restless leg syndrome. Research shows that various SIBO treatments are effective for improving or eliminating these conditions. However in many cases there is no available research involving probiotics.

Can we say with any certainty that probiotics will be effective for treating these SIBO-related conditions? No. However, probiotics are a safe and affordable treatment option for SIBO. Taking probiotics for SIBO is recommended, and this approach may provide relief from these related symptoms and conditions.


In this study, SIBO patients presented with a higher rate of rosacea when compared to healthy controls. 93% of SIBO patients with rosacea experienced an improvement or complete elimination of rosacea symptoms after SIBO treatment [5].

Non-Responsive Celiac Disease

For most SIBO patients with celiac disease, a gluten-free diet resolves gastrointestinal symptoms. One study showed underlying SIBO affected most celiacs with persistent gastrointestinal symptoms. After SIBO treatment, all patients were symptom-free one month later [6]. However, in rare cases, celiac patients can continue to experience gastrointestinal distress (bloating and constipation) when following a gluten-free diet.

Rheumatoid Arthritis

Joint pain is a common symptom we hear about in the clinic. Research shows a connection between gut imbalances, dysbiosis, and rheumatoid arthritis [7]. Patients with rheumatoid arthritis who followed a two-week elemental diet (a therapy commonly used for SIBO patients) demonstrated improved stiffness and pain [8].

Mood Improvements

Research shows that gut health has a significant impact on brain function and mood [9]. In patients with mild to moderate depression, probiotic treatments have resulted in considerable mood improvement [10].

Restless Leg Syndrome

A study found 59% of restless leg patients (RLS) tested positive on a SIBO breath test [11].

In a small study, 13 patients were treated for IBS and restless leg syndrome. Ten of the 13 patients saw a minimum of 80% improvement in their RLS symptoms [12].

Finding a Quality SIBO Probiotic

With so many probiotic supplement options on the market, you might wonder where to start. Here’s advice to help simplify your probiotic shopping experience.

Almost every probiotic can be classified into one of three categories:

3 Categories of Probiotics

Research shows that treating IBS and SIBO with a multispecies probiotic approach provides a synergistic effect that may work better than taking only one type of probiotic [13].

We have seen the best results in SIBO patients whose treatment protocol includes probiotic species from each of these three categories. For some SIBO patients who have been unsuccessful with probiotics, this Triple Probiotic Therapy makes all the difference.

It’s very important to choose high-quality probiotic supplements, as research shows that many probiotic supplements don’t live up to label claims [14, 15]. When shopping for probiotics, look for products that meet these standards:

  • Clearly list probiotic species
  • Label states colony-forming units (CFUs) in the billions
  • Label displays a clear manufactured date and expiration date
  • Free of allergens (gluten-free, vegan, non-GMO)
  • Good Manufacturing Practices (GMP) certification
  • Lab-tested and verified for species and potency

SIBO Probiotics and Treatment Planning

man and woman with a doctor

Treating SIBO with a probiotic protocol is a simple approach that’s often overlooked. For most patients with gut dysbiosis, we recommend starting treatment with three foundational approaches: diet, lifestyle, and probiotics. Additional treatments are available if these approaches do not relieve all of your symptoms. 


If you aren’t already doing so, choose fresh, unprocessed, anti-inflammatory foods. A healthy diet provides the starting point for a healthy microbiome. The Paleo diet provides an excellent framework for you to start. 

For others, implementing a short-term low FODMAP elimination diet may be necessary. The low FODMAP diet provides a framework for the temporary elimination of fermentable carbohydrates that contribute to SIBO symptoms (distension, leaky gut, and abdominal pain).



When combined with eating a healthy diet and taking probiotics, regularly practicing stress management techniques (meditation, journaling, etc.) can help manage SIBO symptoms. 

Poor sleep

A lack of sleep can adversely impact your gut health [16]. Getting adequate sleep is a foundational pillar of good gut health. 


Moderate exercise has been shown to be beneficial for a healthy immune system and microbiome [17, 18]. We recommend choosing low to moderate-intensity exercises, such as walking, jogging, bicycling, and yoga.  


For some SIBO patients, the foundational approaches of diet, lifestyle, and probiotics are adequate to reduce and relieve symptoms. For others, additional therapies may need to be considered.

Prokinetics are agents that support healthy motility (moving food through the stomach and intestinal tract). If motility is slow, constipation can occur. If motility is too fast, it can experience diarrhea. Impaired motility can contribute to bacteria and fungal overgrowth.. 

Prokinetics have a balancing effect on the digestive tract and can be effective for patients with both diarrhea and constipation. 

brown capsules in a bowl and in a spoon

Antimicrobial and Antibiotic Therapy

Herbal antimicrobials and/or antibiotic therapy are targeted therapies intended to kill off excessive bacterial growths. These are both a standard approach for treating SIBO.  

Herbal antimicrobials: In functional medicine, herbal antimicrobials are more commonly used than prescription medications. Herbal antimicrobials have demonstrated effectiveness in treating IBS and SIBO [19, 20].

Herbal antimicrobials may also have beneficial side effects: 

  • Anti-inflammatory and anti-depressant properties [21, 22]  
  • The treatment of bacterial and fungal imbalances such as candida overgrowth [23

Prescription antibiotics: Rifaximin is an antibiotic commonly used as a SIBO treatment. Research shows that Rifaximin eliminates SIBO for 67% of patients [24].

Elemental Diet

The final step to consider if other treatment interventions have not been successful is the elemental diet. This diet was developed specifically as a therapeutic tool for patients with severe digestive conditions. While most research has focused on using the elemental diet for inflammatory bowel disease, one study of SIBO patients showed that a two-week elemental diet normalized lactulose breath tests in 80% of SIBO patients [25]. 

SIBO can present differently in each patient. To recover, some SIBO patients may need a personalized approach that includes dietary changes, lifestyle modifications, SIBO probiotics, prokinetics, and antimicrobial therapies. 

Bottom Line

Regardless of what the internet may have you believe, probiotics can be an effective part of an overall strategy to treat small intestinal bacterial overgrowth. Using one SIBO probiotic from each category (lactobacillus, saccharomyces boulardii, and bacillus) can be a very effective way to treat dysbiosis and manage SIBO symptoms. 

Probiotics are an accessible, cost-effective treatment choice and have been shown to be beneficial for a wide range of digestive and non-digestive symptoms.

Contact us today if you have questions about SIBO probiotics or you’d like our help with developing a SIBO treatment plan. 


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