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Prebiotics and FODMAPs may improve antimicrobial treatment for SIBO

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Alon Blumgart ● 3 min read

Small intestinal bacteria overgrowth (SIBO) is thought to affect up to 80% of irritable bowel syndrome (IBS) patients. SIBO causes inflammation both in the gut and systemically, which is why it is a contributing factor to many chronic diseases.[1,2] It is also notoriously difficult to treat, with high relapse rates, so finding new treatment protocols for SIBO is hugely beneficial.[3]

The treatment of SIBO is complex and multifaceted, involving diet and lifestyle changes, removing drivers of the condition, decreasing symptoms, addressing inflammation and, most importantly, clearing the bacterial overgrowth in the small intestine.[1-4]

Rifaxamin is the most commonly used antibiotic for treating SIBO. It is a locally acting antibiotic in the small intestine.[3-6] Figures vary on its efficacy, with some rates as high as 87% for hydrogen dominant SIBO and 85% for methane dominant SIBO, when combined with neomycin.[3-7] 

Herbal antimicrobials are also commonly used to treat SIBO, with one study showing efficacy rates similar to that of rifaxamin.[8] One study aimed to determine if rifaxamin administration alongside partially hydrolysed guar gum (PHGG) supplementation is better than rifaxamin alone; it was scored by a glucose breath test (GBT) and symptom reduction questionnaire. PHGG is a soluble fibre derived from guar gum with a lower molecular weight, which allows it to be conveniently used as a capsule or powder. This also makes it soluble in water, tasteless and odourless. [3]

In this study, a 50g glucose breath test was given to 500 consecutive patients with IBS-type symptoms. Patients with a positive glucose breath test and predisposing conditions to SIBO entered into the study, and were randomised to receive rifaximin 1200mg/day or rifaximin 1200mg/day and PHGG at 5g/day for 10 days. Patients completed a symptom questionnaire and GBT both in the basal condition and 1 month after withdrawal of therapy. 

Eradication rate of SIBO was 62.1% (23/77) in the rifaximin group and 85% (34/40) in the rifaximin plus PHGG group. Clinical improvement was observed in 86.9% and 91.1% of eradicated cases in rifaximin and rifaximin plus PHGG groups, respectively. [3]

What can we learn from this study as clinicians?

It appears that PHGG increases the efficacy of rifaxamin for treating SIBO. Reasons for this could be:

  1. One of the main causes of SIBO, and its high relapse rates, are disruptions and damage to the migratory motor complex (MMC). The MMC governs gut motility in between meals to help flush out bacteria and prevent bacterial stasis/overgrowth. Food poisoning is thought to be one of the main causes of MMC disruption. PHGG, as a soluble fibre, may increase motility of the small intestine.[1-3,10,11]
  2. PHGG is a prebiotic that increases colonic lactobacilli and bifidobacteria, which tend to be low in IBS patients. Prebiotics are a fuel source for bacteria. Antibiotics/antimicrobials work on the replicating walls of bacteria and bacteria will replicate more when there are food sources available. When food sources are not available, bacteria go into hibernation and they become starving, walled off, distressed and they don’t replicate. They are waiting for conditions to improve again. That’s a survival mechanism. So when the bacteria are in survival mode, antibiotics won’t penetrate and won’t work as well. Therefore, the addition of PHGG may provide a fuel source for overgrown bacteria to replicate, hence increasing antimicrobial efficacy.[3,9] 

SIBIO expert Dr. Pimentel argues that this study may also present a rationale for incorporating foods that exacerbate their IBS symptoms during treatment such as foods high in FODMAPs, as these foods provide fuel for bacteria replication.[9]

The Funari et al study (2010) warrants the use of PHGG during antimicrobial treatment for SIBO; it does not seem harmful and may be very beneficial. However more studies are needed to fully validate this finding. 


  1. Dukowicz AC, Lacy BE, Levine GM. Small intestinal bacterial overgrowth. Gastroenterol Hepatol 2007;3(2):S112-S122. [Full text]
  2. Bures J, Cyrany J, Kohoutova D, et al. Small intestinal bacterial overgrowth syndrome. World J Gastroenterol 2010;16(24):S2978-S2990. [Full text
  3. Furnari M, Parodi A, Gemignani L, et al. 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;32(8):S1000-S1006. [Full text]
  4. Foxx-Orenstein AE. New and emerging therapies for the treatment of irritable bowel syndrome: an update for gastroenterologists. Therap Adv Gastroenterol 2016;9(3):S354-S75. [Full text
  5. Schoenfeld P, Pimental M, Chang L, et al. Safety and tolerability of rifaximin for the treatment of irritable bowel syndrome without constipation: a pooled analysis of randomised, double-blind, placebo-controlled trials. Alimentary Pharmacol Therap 2014;39(10):S1161-S1168. [Full text]
  6. Peralta S, Cottone C, Doveri, et al. Small intestine bacterial overgrowth and irritable bowel syndrome-related symptoms: Experience with Rifaximin. World J Gastroenterol 2009;15(21):S2628-S2631. [Full text]
  7. Low K, Hwang L, Hua J, et al. A combination of rifaximin and neomycin is most effective in treating irritable bowel syndrome patients with methane on lactulose breath test. J Clinical Gastroenterol 2010;44(8):S547-S550. [Abstract]
  8. Chedid V, Dhalla S, Clarke J, et al. Herbal therapy is equivalent to rifaximin for the treatment of small intestinal bacterial overgrowth. Glob Adv Health Med 2014;3(3):S16-S24. [Full text]
  9. Chriskresser.com: Interview with Dr. Mark Pimentel, https://chriskresser.com/sibo-update-an-interview-with-dr-mark-pimentel/
  10. Russo L, Andreozzi P, Zito FP, et al. Partially hydrolyzed guar gum in the treatment of irritable bowel syndrome with constipation: effects of gender, age, and body mass index. Saudi J Gastroenterol 2015;21(2):S104-S110. [Full text]
  11. Niv E, Halak A, Tiommny E, et al. Randomized clinical study: Partially hydrolyzed guar gum (PHGG) versus placebo in the treatment of patients with irritable bowel syndrome. Nutr Metab 2016;13(1):S10. [Full text]


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Alon Blumgart

Alon Blumgart is a clinical Naturopath and Nutritionist with a Bachelor of Health Science in Naturopathy (BHSc) from the Southern School of Natural Therapies.

During his studies, Alon developed a passion for gut health and the microbiome. He went on to be accepted into the Bioceuticals Internship Program, where he developed a product concept specific for small intestine bacteria overgrowth (SIBO). 

Alon enjoys guiding his patients to improve their health by helping them implement practical, fad-free, evidence-based diet and lifestyle habits, as well as using herbal and nutritional supplementation based on the most current evidence available. He aims to treat the underlying drivers of health conditions, rather than just focussing on symptoms.