NOTE: This article was originally published on September 8, 2019, and was updated on August 28, 2026. The first article in this series about Small Intestinal Bacterial Overgrowth (SIBO) covers what SIBO is, how common it is, and its primary symptoms. The second article in the series is about Diagnosing Small Intestinal Bacterial Overgrowth (SIBO), and this is the third and final article in the series about treating SIBO, including antimicrobials and dietary changes.
What is the Standard Antibiotic Treatment for SIBO?
The standard treatment for Small Intestinal Bacterial Overgrowth (SIBO) is Rifaximin, a broad-spectrum antibiotic [1,2].
Treatment for Intestinal Methanogen Overgrowth (IMO), formerly called “methane-dominant SIBO,” includes antibiotics such as metronidazole and neomycin prescribed along with Rifaximin [1].
NOTE: As outlined in the first article in this three-part series, since Intestinal Methanogen Overgrowth is caused by single-celled organisms called archaea, and not bacteria, it is classified as IMO, and not SIBO.
How Effective is Antibiotic Treatment in SIBO?
A 2021 systematic review and meta-analysis reported that antibiotic treatment alone with Rifaximin achieves only a ~59% SIBO eradication rate [3], which means that in more than 40% of cases, SIBO persists.
Furthermore, even following successful initial eradication of Small Intestinal Bacterial Overgrowth following a full course of antibiotics, SIBO recurs in approximately 12.6% of patients at 3 months, 27.5% at 6 months, and 43.7% at 9 months [4].
What Are the Risk Factors of SIBO Coming Back?
Risk factors for recurrence of SIBO include altered bowel anatomy such as diverticulosis, older age, and long-term use of proton pump inhibitors (PPIs) [1].
The American College of Gastroenterology reported in their 2020 Clinical Guidelines for Small Intestinal Bacterial Overgrowth that PPIs are one of the most commonly prescribed medications used to treat Gastro-Esophageal Reflux Disease (GERD), ulcers, functional dyspepsia, and for people with unexplained GI symptoms [1], and most studies have shown a higher risk of developing SIBO for those taking PPIs [1].
Are Antimicrobials as Effective as Antibiotics for SIBO?
A 2014 study reported that herbal antimicrobial combinations of FC Cidal® with Dysbiocide®, and Candibactin-AR® with Candibactin-BR® can be as effective as the antibiotic Rifaximin in the treatment of Small Intestinal Bacterial Overgrowth [5].
In my years of practice, I have usually seen Physicians (MDs) prescribe the antibiotic Rifaximin for the treatment of Small Intestinal Bacterial Overgrowth, and naturopaths prescribe one of the pairs of herbal antimicrobials, either FC Cidal® with Dysbiocide®, or Candibactin-AR® with Candibactin-BR®.
The most frequent protocols I have seen using these antimicrobials are 2 capsules of FC Cidal® and 2 capsules of Dysbiocide®taken twice daily with meals for a month, or 2 capsules of Candibactin-AR® and 2 capsules of Candibactin-BR® taken twice daily with meals for 4-6 weeks. I have also seen naturopaths prescribe the herbal antimicrobial Microcydin® to be taken three times per day with food, for a month.
Can a Dietitian Help with SIBO Treatment?
Yes, a Dietitian can provide a specialized diet that is implemented in three stages, alongside the antibiotics prescribed by a doctor, or antimicrobials prescribed by a naturopath, and that can provide overall symptom relief and improved quality-of-life outcomes compared to antibiotics alone.
A 2010 study found that combining the antibiotic Rifaximin with partially hydrolyzed guar gum (PHGG) increased the eradication rate from 62% to 85%, while also protecting good gut bacteria [6].
Most dietary changes for SIBO include reducing fermentable products called FODMAPs, but the American College of Gastroenterology’s 2020 Clinical Guidelines for Small Intestinal Bacterial Overgrowth indicate that most data on low-FODMAP diets for SIBO are extensions of IBS studies [1]. That said, the ACG’s 2020 Clinical Guidelines for Small Intestinal Bacterial Overgrowth indicated that this data supports that
(1) a low FODMAP diet is associated with fewer fermentation products, as assessed by the breath test,
(2) that daily hydrogen output was much higher when FODMAPS were eaten,
(3) that there is a small decrease in hydrogen production in subjects who consumed a low FODMAP diet, along with decreased symptom severity [1].
Randomized trials of multi-modal approaches, including combining standard antibiotics with a three-stage low-FODMAP diet (Elimination, Reintroduction, and Liberalization), use of herbal antimicrobials, and probiotics, demonstrate better overall symptom control and improved quality-of-life outcomes compared to antibiotics alone [7].
NOTE: Clinical consensus guidelines from the ACG caution against using a strict low-FODMAP diet simultaneously during active antibiotic treatment [1] because bacteria must be metabolically active and fermenting some carbohydrate for antibiotics to be maximally effective [1]. If bacteria are starved using a strict low-FODMAP diet before antibiotics or antimicrobials are started, bacteria may become dormant and resistant to antimicrobial treatment.
Three-Phase Dietary Treatment for SIBO
The following three-phase dietary approach implements the above recommendations.
Phase One – Pre-Treatment Stage: This stage ideally occurs a month before beginning antibiotics or antimicrobials to prepare the digestive environment and does not involve an elimination of all FODMAP foods, because bacteria must be metabolically active and fermenting some carbohydrate for antibiotics or antimicrobials to be maximally effective. Inclusion of PHGG allows for the minimal bacterial activity needed to ensure that when antimicrobial treatment begins, it is more likely to be successful. NOTE: For those who have already started antimicrobial or antibiotic medication, this phase can be implemented immediately, before transitioning to Phase Two for the last two weeks of antimicrobial treatment.
Phase Two – Active Treatment Diet (Total Elimination Diet): This stage occurs during the four-week (or 6-week) course of prescribed antimicrobials or antibiotics and involves knowing the amounts of foods that can be eaten within each category, and those foods that should be avoided.
Phase Three – Post-Treatment Diet (Reintroduction Stage): This phase focuses on the reintroduction of specific FODMAP groups, while continuing to limit ones that could be problematic. It also teaches how to gradually liberalize the diet, providing a sustainable way to eat while reducing the risk of SIBO recurrence. NOTE: Professional dietary guidance prevents unnecessary long-term low-FODMAP restriction, which can negatively impact the gut microbiome by reducing good gut bacteria, including Bifidobacteria.
Clinical Reflections
The literature supports implementing a three-stage low-FODMAP diet (Elimination, Reintroduction, and Liberalization) in progressive stages while taking either antibiotics or herbal antimicrobials, or immediately afterwards for better overall symptom control and improved quality-of-life outcomes. This article outlines effective treatment options, and the first article in the series outlined what SIBO is, and the second article explained how it is diagnosed.
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Quick Clinical Summary
Q: Does a low-FODMAP diet cure SIBO?
A: No. While a low-FODMAP diet is excellent for managing symptoms by reducing the ‘fuel’ for bacteria, it does not eradicate the overgrowth in the small intestine. Clinical eradication requires antimicrobial or antibiotic treatment.
Q: Why is Partially Hydrolyzed Guar Gum (PHGG) used in SIBO treatment?
A: PHGG is a prebiotic fiber that has been shown to increase the success rate of SIBO eradication. Research indicates that adding PHGG to Rifaximin therapy increases the eradication rate from 62% to 85% by keeping bacteria active and more susceptible to the treatment.
Q: What are the common causes of SIBO recurrence?
A: Recurrence occurs in nearly half of patients within a year if the root causes are not addressed. These can include low stomach acid (often from long-term PPI use), pancreatic insufficiency, or motility disorders.
References
- Pimentel M, Saad RJ, Long MD, et al. (2020). ACG Clinical Guideline: Small Intestinal Bacterial Overgrowth. American Journal of Gastroenterology, 115(2), 165–178.
- Ghoshal UC, Sachdeva S.; Ghoshal U. et al. Asian-Pacific consensus on small intestinal bacterial overgrowth in gastrointestinal disorders: An initiative of the Indian Neurogastroenterology and Motility Association. Indian J. Gastroenterol. 2022, 41, 483–507
- Wang J, Zhang L, Hou X. Efficacy of rifaximin in treating small intestine bacterial overgrowth: a systematic review and meta-analysis. Expert Rev Gastroenterol Hepatol. 2021 Dec;15(12):1385-1399. doi: 10.1080/17474124.2021.2005579. Epub 2021 Nov 26. PMID: 34767484.
- Lauritano EC, Gabrielli M, Scarpellini E, Lupascu A, Novi M, Sottili S, Vitale G, Cesario V, Serricchio M, Cammarota G, Gasbarrini G, Gasbarrini A. Small intestinal bacterial overgrowth recurrence after antibiotic therapy. Am J Gastroenterol. 2008 Aug;103(8):2031-5. doi: 10.1111/j.1572-0241.2008.02030.x. PMID: 18802998.
- Chedid V, Dhalla S, Clarke JO, et al. Herbal therapy is equivalent to rifaximin for the treatment of small intestinal bacterial overgrowth. Global Advances in Health and Medicine. 2014 May;3(3):16-24. [https://doi.org/10.7453/gahmj.2014.019]
- Furnari M, Parodi A, Gemignani L, Giannini EG, Marenco S, Savarino E, Assandri L, Fazio V, Bonfanti D, Inferrera S, Savarino V. Clinical trial: the combination of rifaximin with partially hydrolysed guar gum is more effective than rifaximin alone in eradicating small intestinal bacterial overgrowth. Aliment Pharmacol Ther. 2010 Oct;32(8):1000-6. doi: 10.1111/j.1365-2036.2010.04436.x. Epub 2010 Aug 18. PMID: 20937045.
- Redondo-Cuevas, L., Belloch, L., Martín-Carbonell, V., Nicolás, A., Alexandra, I., Sanchis, L., Ynfante, M., Colmenares, M., Mora, M., Liebana, A. R., et al. (2024). Do Herbal Supplements and Probiotics Complement Antibiotics and Diet in the Management of SIBO? A Randomized Clinical Trial. Nutrients, 16(7), 1083. https://doi.org/10.3390/nu16071083
I am a Registered Dietitian Nutritionist and the owner of BetterByDesign Nutrition Ltd. With a postgraduate degree in Human Nutrition and a background as a published mental health nutrition researcher, I have been dedicated to supporting my clients’ clinical needs since 2008.
I hold active professional licenses in BC (CHPBC), Alberta (CDA), and Ontario (CDO), allowing me to provide regulated Medical Nutrition Therapy across these provinces. My expertise spans chronic disease management, complex digestive health, and therapeutic diets. I am deeply passionate about helping people reclaim their health, rooted in my firm belief that Nutrition is BetterByDesign©.