Treating Small Intestinal Bacterial Overgrowth (SIBO)

In the first article in this series about Small Intestinal Bacterial Overgrowth (SIBO) I covered what SIBO is, how common it is, as well as its symptoms. In the second article, I outlined different tests used to diagnose SIBO, some of the challenges with those, the difference between hydrogen-dominant and methane-dominant SIBO, and why Irritable Bowel Syndrome (IBS) that does not improve despite adopting appropriate dietary changes may be SIBO.  In this article (which is part 3 in the series), I outline the main dietary approaches used in treating SIBO along with antibiotic and evidence-based herbal antimicrobial therapy, and elaborate as to whether dietary changes should come before- or after antimicrobial treatment.

In discussing the treatment of Small Intestinal Bacterial Overgrowth, it’s important to keep in mind that SIBO is the presence of types of bacteria in the small intestine that are not supposed to be there.  While dietary changes can help by improving the symptoms, in and by themselves they will not result in the elimination of the bacteria that are contributing to the symptoms. The bacteria that are foreign to the small intestine need to be eradicated and the underlying cause of the SIBO needs to be addressed. As outlined in the first article, Small Intestinal Bacterial Overgrowth may be caused by a number of conditions, including low stomach acid (achlorhydria), pancreatic insufficiency, anatomical abnormalities such as small intestinal obstruction, diverticula, or fistula (which are abnormal connections between an organ and the intestine), as well as slowing of intestinal movements (motility disorders) that are common in those with diabetes mellitus, as well as due to alcohol consumption and a number of other factors. Addressing those underlying causes is needed, along with correcting intestinal flora imbalance.

NOTE: As a Dietitian, my role is to support treatment of a diagnosed condition from a dietary perspective, but not to diagnose. Diagnosis is the realm of medicine, and diagnosis of SIBO is for a gastroenterologist or Functional Medicine MD to make, using established medical testing protocols. It is also the role of MDs to prescribe antimicrobials.  I provide dietary support during the three phases of treatment with the goal of reducing the person’s symptoms, increasing the likelihood of eradication during antimicrobial treatment, and reducing the likelihood of recurrence of SIBO after eradication.

There are two important factors to keep in mind when it comes to Small Bacterial Overgrowth treatment; (1) despite antibiotic treatment, an older (2008) study found that recurrence of SIBO as diagnosed by glucose breath tests occurs in almost half of all people within a year of treatment [1], however individuals in this study that relapsed were older aged (which is associated with decreased stomach acid), and had a history chronic use of proton-pump inhibitor medication (which also results in lower stomach acid), (2) addressing the underlying cause of SIBO is necessary, otherwise recurrence is likely.

Three Phases of Dietary Treatment for SIBO

Some clinicians take a single dietary approach with SIBO and prescribe one of several low fermentable carbohydrate diets; either a low-FODMAP diet or the Specific Carbohydrate Diet (SCD), or some combination or variation of these. These diets limit the food sources for bacterial that live in the gut (both small and large intestine), thereby reducing symptoms and at first glance, this may seem like an effective approach, except it has two drawbacks;

  • following a diet low in fermentable carbohydrate for periods of longer than a month has been shown to also reduce beneficial bacteria in the gut, such as bifidobacteria [2].
  • Some researchers such as Dr. Mark Pimentel’s group at the Gastrointestinal Motility Program at Cedars-Sinai Medical Center suggest that some fermentable carbohydrates remain in the diet while treating with antimicrobials based on the concept that bacterial are easier to eradicate when they’re active. Antimicrobials act on the replicating cell wall of bacteria, so when bacteria are being starved, they aren’t replicating.

A 2010 study found that treatment of SIBO with the first-line antibiotic Rifaximin alone was only 62% effective, however when Rifaximin was combined with a specific fermentable carbohydrate called partially hydrolyzed guar gum (PHGG), eradication rate was 85% [3]. In addition, the addition of PHGG during the antibiotic treatment phase also prevented the eradication of both of the beneficial bacteria lactobacilli and bifidobacteria from the large intestine.

I take a 3-phase approach to dietary support treatment of SIBO.

Phase I

A first phase of dietary treatment includes the use of a low fermentable carbohydrate diet for 4-6 weeks which enables people to begin to feel better. This is of huge importance to quality of life, after so long of feeling quite unwell! By also including the addition of partially hydrolyzed guar gum (PHGG) in the diet, it allows for the small amount of bacterial growth needed so that once the person is treated with antimicrobials, it is likely to be more successful.

Use of PHGG is also well-known to reduce the symptoms of IBS in both the constipation and diarrhea subtypes [4,5] and since most people with SIBO experience one of these symptoms, or both alternating, addition of PHGG is also beneficial for helping people feel much better, while preparing for the antimicrobial treatment phase.

Phase II

The second phase of dietary treatment coincides with the 4-week period of antimicrobial treatment prescribed by the gastroenterologist or Functional Medicine MD. During this phase, the low fermentable carbohydrate diet is maintained along with the PHGG intake, but begins to include some additional fermentable carbohydrate food, as tolerated. This helps feed the bacteria just enough so that the antimicrobials are more likely to be effective, but without making the person feel unwell.

As mentioned above, studies have shown that the antimicrobials along with PHGG may result in up to 85% eradication[3], a study from 2009 found that eradication rates with Rifaximin alone is only about 50% [6]. It is thought that this may be due to a failure to distinguish between hydrogen-positive and methane-positive types of SIBO.  In methane-positive SIBO, eradication has been found to be as high as 85% when Rifamixin is combined with another antibiotic, Neomycin [7]. In methane-positive SIBO, Dr. Pimentel and his group recommend 550 mg Rifaximin three times per day in combination with neomycin 500 mg twice a day for 14 days, or Rifaximin 550 milligrams three times per day with Metronidazole 250 milligrams three times per day for 14 days [8].

Antimicrobials prescribed by some MDs may include herbal antimicrobials. Herbal antimicrobials (FC Cidal® with Dysbiocide® or Candibactin-AR® with Candibactin-BR®) were shown in a 2014 study to be even more effective in eradication of SIBO bacteria as Rifaximin [8]. Of those treated with one of the herbal therapy combinations, 46% of subjects had a negative result upon re-testing, whereas only 34% of those using Rifaximin had a negative result upon re-testing. Furthermore, approximately 57% of those who failed to achieve eradication on Rifaximin as measured by repeat breath testing, achieved eradication on one of the two herbal antimicrobial regimens [8]. Also of significance, in 2014 when the study was conducted, standard treatment with a 4-week supply of Rifaximin (two 200 mg Rifaximin tablets 3x daily) cost $1247.39, whereas the cost for the herbal therapy (2 capsules twice daily of either treatment) was no more than $120 for a one-month supply [9]. The high treatment response rate of the herbal formulations, reduced cost of treatment and long term Generally Recognized As Safe (GRAS) safety record of specific herbs used in the formulations [8], and the fact that these supplements can be purchased by the general public without a prescription provides individuals and their practitioners with several treatment options.

Phase III

The last phase of dietary treatment is the gradual liberalization of the low-fermentable carbohydrate diet. After antimicrobial treatment, once the gut microbiome has been restored, a person should be able to tolerate a healthy, whole food diet. That said, it may be advantageous for a person who has had SIBO previously to continue to avoid unnecessary additions to the diet such as sugar alcohols (xylitol, erythritol, etc.) or gums such as carrageenan, xanthan gum and guar gum (not to be confused with hydrolyzed guar gum!), as well as to limit high fructose and lactose intake.

However, if a person begins to have symptoms again, then having a new hydrogen breath run to ensure there is no recurrence of SIBO makes sense. If the breath test is negative, then further medical investigation for other underlying causes of causes, including low stomach acid, pancreatic insufficiency or intestinal motility disorders may be next. Given that no other underlying cause is identified, food intolerances , including histamine intolerance, A1 beta-casein intolerance might be worth evaluating.

Final Thoughts

SIBO, like IBS is not easy-to-diagnose. More clear-cut diagnoses such as IBD, celiac disease, food allergies etc. need to be ruled out first and while IBS has now gained acceptance as a “real” diagnosis, SIBO is still one of those in which there is much debate.

I have more confidence in the jejeunal aspirate method of diagnosis and wonder if the breath tests really measure what they purport to measure. That said, when people previously diagnosed and unsuccessfully treated for IBS are treated with diet plus antimicrobials, many get better. Are IBS and SIBO really two diagnoses or one?

A low fermentable carbohydrate diet has long been used in the treatment of IBS and the use of partially hydrolyzed guar gum has a successfully and safe long-term history in the treatment of IBS), so continuing to use these in the treatment of SIBO, along with evidence-based antimicrobial treatment prescribed by an MD is a sensible and safe approach.

The Gut Microbiome – so much to learn

There is so much we are discovering about the gut microbiome (the bacteria in our intestines that we live in symbiosis with) and the relationship between alterations in the gut microbiome and chronic disease.

For example, a study published on June 19, 2019 in the journal Pain [10] found a correlation between fibromyalgia (another one of those diseases that medical professionals debate the legitimacy of) and abnormalities in the gut microbiome. In this study conducted in Montreal, approximately  20 different species of bacteria were found to be abnormally high, or abnormally low in the microbiomes of subjects suffering from the disease, compared with healthy controls. It was found that “fibromyalgia and the symptoms of fibromyalgia — pain, fatigue and cognitive difficulties – contribute more than any of the other factors to the variations we see in the microbiomes of those with the disease” [11].

There is much we don’t know in terms of IBS and SIBO but at the end of the day, there are people suffering with these conditions whose quality of life is greatly affected. If the best we have to offer people diagnosed with SIBO at this time is the use of a low fermentable carbohydrate diet along with the addition of well-studied PHGG used in conjunction with antimicrobial agents prescribed by a physician — and this helps people feel significantly better, then this is the most evidence-based approach we have at this time.

More Info?

If you would like to know more about the hourly consultations and packages I provide, including SIBO support, then please click on the Services tab or have a look in the Shop. If you would like additional information, please send me a note using the Contact Me form above, and I will reply as soon as I can.

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LEGAL NOTICE: The contents of this blog, including text, images and cited statistics as well as all other material contained here (the ”content”) are for information purposes only.  The content is not intended to be a substitute for professional advice, medical diagnosis and/or treatment and is not suitable for self-administration without the knowledge of your physician and regular monitoring by your physician. Do not disregard medical advice and always consult your physician with any questions you may have regarding a medical condition or before implementing anything  you have read or heard in our content.


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  3. Furnari M, Parodi A, Gemignani L, Clinical trial: the combination of rifaximin with partially hydrolysed guar gum is more effective than rifaximin alone in eradicating small intestinal bacterial overgrowth, Alimentary Pharacology and Therapeutics, Volume 32(8) August 2010, page 1000—1006
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