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Small Intestinal Bacterial Overgrowth: Part 2

In part one of our small intestinal bacterial overgrowth (SIBO) blog post, we defined SIBO and discussed risk factors and diagnostic testing. This blog post will focus on treatment. The 5R framework, a comprehensive approach to gut-healing, is the protocol used by functional medicine practitioners to treat gut imbalance and dysfunction, including SIBO. The five R’s stand for: Remove, Replace, Reinoculate, Repair, and Rebalance. The goal of SIBO treatment is to identify and treat any underlying causes, eradicate the overgrowth of bacteria, and provide nutritional support. 


It is crucial to identify and remove anything that could be contributing to or causing dysfunction in the digestive system. Since SIBO is caused by an overgrowth of bacteria in the small intestine, treatment aims to reduce bacteria to a normal level. Although there are no FDA-approved medications specifically for SIBO, there are prescription and nonprescription options that have been studied in individuals with SIBO and shown to be effective, including antibiotics,1 herbal supplements, and nutraceuticals.2 Your functional medicine practitioner can work with you to determine what course of antibiotic therapy and/or herbal supplements may be appropriate for you. 

As part of the remove step, certain dietary changes to remove potentially problematic foods from the diet can help with symptoms. Diets that have shown to be helpful in SIBO include the Specific Carbohydrate Diet (SCD), Elemental Diet, Low FODMAP Diet, or a combination of the aforementioned diets.3,4 It’s also advised to remove inflammatory foods to aid in healing the gut lining. See this link to read a previous blog post discussing the effects of diet on gut health.


Your gut may be lacking in digestive enzymes and acids, key components in digestion and absorption of nutrients as well as natural defenses against bacterial overgrowth. Replacing enzymes and acids is important for SIBO treatment and to prevent recurrence. Supplementing with digestive enzymes, bitters, bile acids, or hydrochloric acid may be appropriate. If there are any vitamin or mineral deficiencies, those should be corrected as well. 

In those with constipation, prokinetics may be recommended to help speed up transit time. A study found that patients with SIBO are more likely to have prolonged bowel transit time in their small intestine, which means that taking a medication or supplement that promotes gut motility could benefit some SIBO patients.5


Feed the beneficial bacteria in the gut with pre- and probiotic foods and supplements to help re-establish a healthy gut microbiome. Probiotics seem to help with GI-related symptoms and improve eradication rates when combined with antibiotics during SIBO treatment.6,7 Foods like raw sauerkraut, kimchi, and kefir contain natural probiotics and high soluble fiber foods (prebiotics) provide food for the friendly bacteria so they can flourish.  When introducing pre- and probiotics, it’s advised to start with a low dose and go slow while working up to the desired dose. See these links to previous blog posts to read more about probiotics: Probiotics 101Probiotics FAQ: Part 1, and Probiotics FAQ: Part 2


The mucosal lining of the GI tract serves as a protective barrier, an extremely important function that keeps harmful compounds from entering the bloodstream.  There are numerous factors that can cause increased intestinal permeability (leaky gut), including SIBO.  Support healing of the gut lining by incorporating key nutrients and herbs that soothe, repair, and regenerate. Omega 3’s,8 L-glutamine,9-11 aloe,12-15 and zinc16,17 all have gut-healing properties and there are commercially available preparations containing combinations of these compounds. 


To promote continued gut healing and a balanced microbiome, lifestyle factors must be evaluated and addressed.  Sleep, exercise, stress, and relationships can all affect the GI tract. Optimizing these areas of life should not be overlooked when treating gut imbalance and dysfunction. 

If you are interested in learning more about gut restoration, our team of functional medicine pharmacists at PharmToTable are here for you.  We developed a short questionnaire that can help determine if gut testing and gut restoration may be appropriate for you. After you complete the questionnaire, we’ll send you a free download with our probiotic and digestive enzyme favorites! Also, we’d love for you to join one of our discovery classes or book an appointment to work with us!

Written by Kristina Burban, PharmD during her internship with our team.


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  2. Chedid V, Dhalla S, Clarke JO, et al. Herbal therapy is equivalent to rifaximin for the treatment of small intestinal bacterial overgrowth. Glob Adv Health Med. 2014;3(3):16–24. doi:10.7453/gahmj.2014.019
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  14. Gawron-Gzella, A., Witkowska-Banaszczak, E. et al. [Herbs and herbal preparations applied in the treatment of gastric hyperacidity, gastric and duodenal ulcer in cigarette smokers]. Przegl Lek. 2005; 62(10):1185-1187
  15. Yusuf, S., Agunu, A. et al. The effect of Aloe vera A. Berger (Liliaceae) on gastric acid secretion and acute gastric mucosal injury in rats. J Ethnopharmacol. 2004; 93(1):33-37.
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