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The 3 common questions on SIBO treatment and answers that may surprise you:

Q 1. Don’t we need antibiotics for SIBO as low fermentable carbohydrate diets do not “eradicate” an overgrowth in the small intestine?

Q 2. I am worried about being on low-FODMAP, low-carb diet, Fast Tract Diet, etc. for a long time because I don’t want the bacteria in my large intestine to be negatively impacted. What is your take on this?

Q 3. Since happy and well fed SIBO bacteria are easier to kill with antibiotics, isn’t a diet that starves these bacteria the wrong approach when taking antibiotics? Won’t the bacteria go into hiding and become more difficult to eradicate? Shouldn’t we consume more FODMAPs and carbohydrates during antibiotic treatment?

Answer to Question 1

Myths on SIBO Treatment Antibiotics are not guaranteed to “eradicate” the overgrowth.  You can refer to the Target 1 and 2 results and my recent blog for more info on rifaximin, the most commonly prescribed SIBO antibiotic.

When it comes to SIBO and dysbiosis, I prefer the term “control” over “eradication”. If you “eradicate” SIBO, you will be also eradicating the commensal bacteria (good bacteria) that are naturally present in the small intestine. Though fewer in number, these protective commensal bacteria should be preserved for healthy digestion.  Antibiotics used for SIBO are broad spectrum and kill or inhibit a wide range of bacterial types which will include many innocent bystanders. And while some important commensals will be impacted, some of the symptom-causing bacteria will already be or become resistant and persist.

Regarding SIBO diets, the elemental diet is most effective for SIBO because it is a pre-digested formula that contains no hard-to-digest fermentable carbohydrates (only glucose). The diet also achieved 85% SIBO eradication (if you like the word “eradicate”). This result compares favorably over rifaximin which achieved a success rate of 41% vs 32 % placebo (Target 1 and 2). While the elemental diet was effective, it has several drawbacks including cost, unpleasant taste, absence of whole / solid foods and containing very little fat. Also, the argument could be made that increasing predigested fats (fatty acids) and protein (amino acids) over glucose in an elemental diet formulation might be better for advanced cases of SIBO given that glucose can potentially feed SIBO much more efficiently than amino acids and fatty acids.

My recent blog article also references significant improvements by limiting fiber, fructose and lactose as well as using low FODMAP or low-carb diet for SIBO/IBS-related symptoms.

Except the elemental diet, most dietary approaches do not limit the full range of fermentable carbohydrates described in the Textbook of Primary and Acute Care Medicine.  This could hinder their effectiveness for controlling SIBO. However, The Fast Tract Diet (FTD) is designed to quantitatively limit, but not eliminate all five types. The FTD also includes Gut Friendly Practices as well as strategies to identify and address your specific underlying cause(s). Our consultation program uses the same 3 pillar approach to provide customized solutions for your specific SIBO and related conditions.

Question 2

“I am worried about being on low-FODMAP, low-carb diet, Fast Tract Diet, etc. for a long time because I don’t want the bacteria in my large intestine to be negatively impacted.  What is your take on this?”


Myths on SIBO Treatment One thing is clear. Significant reduction of fermentable carbohydrates in your diet is an effective intervention for SIBO. But what happens to bacteria and their end products in the large intestine when you are on a low carb diet for a long time?

Clearly you would expect fewer bacteria and less of their end products including short chain fatty acids such as butyrate. This is a natural chain of events because you are reducing bacteria’s primary fuel source, carbohydrates. But that does not mean that bacteria in your large intestine are negatively impacted. And here is why they are not.

Changes in Short Chain Fatty Acid – Butyrate

Butyrate has important functions including anti-inflammatory properties and feeding cells that line the large intestine. But how should we interpret butyrate concentrations in fecal samples?

This study highlighted a drop in certain strains of bacteria and short chain fatty acids (SCFAs) including butyrate in participants on a low carbohydrate diet. But the level of butyrate was measured in fecal samples and was still 8.5 mM. While this represented a 50% reduction compared to the high carb diet, what does this really mean? To me this suggests that butyrate and the other SCFAs are still being produced in excess of what our body needs. Hence they are released in the stool. So I do not see any issue here.

See my response to Jeff Leach’s blog article: Sorry low carbers, your microbiome is just not that into you

Mucosal Atrophy with Intravenous Feeding

Myths on SIBO Treatment Mice fed either a fiber deficient diet or the elemental diet intravenously  (i.e. bypassing the gut entirely) resulted in epithelial barrier dysfunction and translocation (moving from the gut to the bloodstream) of gut bacteria. The cause was proposed to be something called mucosal atrophy – dying of the mucosal lining. These findings raised a concern that this could be a problem with people using the elemental diet. But a study in humans found that this is not the case. The study found no more bacterial translocation than the control group. The same conclusions were reached in this broader review of the topic. Even in the most carb-limiting situation, mucosal damage in mice was not mirrored in humans.

How Your Microbiota Is Being Fed

Unlike the elemental diet, real food diets low in fermentable carbs still provide many species of fermentable carbohydrates. Look at the large number of people who have been on a ketogenic diets for many years. If low carbohydrate diets were causing significant damage to the bacteria in the large or small intestine, you would think we would have heard something about it, at least in some individual case studies.

Even if you eliminated all carbohydrates from your diet, you would not starve your microbiota. This is because:

  • Your body continues to product mucus. Mucus is 80% carbohydrate but also contains sialic acid. Sialic acid is a glycoprotein meaning that mucus provides not only a carbon energy source (carbohydrate), but also a source of nitrogen (protein/amino acid) which is required by bacteria.
  • Bacteria can also ferment 20% of dietary protein which escapes digestion thus ensuring its availability for bacteria.
  • Consuming animal-based foods also feeds your gut bacteria with “animal fiber”.  This is comprised of fermentable elements such as undigested skin, bone, cartilage, collagen and other glycans. Though potentially unsafe in modern times, our ancient ancestors included even more animal fiber by  consuming raw meat. For more info, refer to “Duck Dodger’s” comments at the end of my resistant starch article.

In support of the idea that we, and presumably our microbiota can stay healthy with few carbs I found the study of two men who ate nothing but meat for one year with no ill effects to be an interesting read.

Take Home Message

Our bodies and our microbiota are adaptive to capitalize on the nutrients available. After all, our microbiota evolved to help us avoid starvation over many thousands of years. This implies that our microbiota should be fairly robust in the face of dramatic reductions not only in carbohydrates, but in all three food groups. To date, I have found no evidence that low carb diets damage our microbiota or our general health.

The Fast Tract Diet quantitatively reduces, but does NOT eliminate fermentable carbohydrates. The range is from 20 to 45 grams plus per day depending on the severity of your symptoms. Once you get SIBO under control, the damage done to your small intestine should begin to heal. As healing progresses, your carbohydrate tolerance will improve over time and allow for the gradual increase fermentable carbohydrates in your diet.

Question 3

Since happy and well fed SIBO bacteria are easier to kill with antibiotics, isn’t a diet that starves these bacteria the wrong approach when taking antibiotics? Won’t the bacteria go into hiding and become more difficult to eradicate? Shouldn’t we consume more FODMAPs and carbohydrates during antibiotic treatment?


Fast Tract Digestion IBSLet’s not forget that antibiotic use itself is linked to developing functional gastrointestinal disorders.  And I do NOT advocate antibiotics as a first line therapy for treating SIBO and related conditions. But assuming that antibiotic treatment is warranted, I would still suggest consuming fewer fermentable carbohydrates as recommended in the Fast Tract Diet while taking them.

Here Is Why

The feed to kill concept is interesting. I have read the study about using guar gum with rifaximin for SIBO. The 15% increase in SIBO eradication is certainly something to consider and merits further study. But adding this single species of fiber during treatment is very different from increasing FODMAPs or overall carbohydrates during treatment.

While actively growing (i.e. well fed) bacteria do tend to be more susceptible to the effects of antibiotics, the type of antibiotic matters. For example, ciprofloxacin kills actively growing bacteria better than non-growing bacteria, but daptomycin, a different kind of antibiotic kills bacteria regardless. Also, the specific bacterial species causing your case of SIBO will impact the efficacy of antibiotics. And the type of supplemental fiber may also influence the degree of antibiotic susceptibility.

Myths on SIBO Treatment Even more importantly, there is a powerful rational for limiting overall fermentable carbohydrate levels during antibiotic treatment. This recent study led by Justin Sonnenburg provides a compelling explanation for why people taking antibiotics are more susceptible to infection with pathogens (bad bacteria) such as Salmonella and Clostridia difficile. It’s all about a spike in available carbohydrate levels.

This is what happened. When researchers gave mice antibiotics, the mice became more susceptible to infection by pathogens. They also measured a dramatic spike in a sugar called “sialic acid”, a normal component of mucus which commensal (good) bacteria use for fuel.

With antibiotics, there were fewer commensals (good bacteria) available to use the sugar because they were killed by antibiotics, and the levels of sugar soared. The pathogens were able to access this fuel source and set up shop. In Sonnenberg’s own words “Pathogens take advantage of a temporary spike in available sugars liberated from intestinal mucus left behind by slain (killed) commensal microbes”.

If you imagine a similar scenario playing out in our bodies – humans have similar sialic acid containing mucus, it seems to me that you would want to be very careful about adding more carbohydrate fuel to the potential fire.

My recommendation is to avoid antibiotics unless absolutely necessary. When they are used, limit overall fermentable carbohydrate levels as recommended by the Fast Tract Diet.

This is the third article on SIBO. If you liked this article, you may want to read:

SIBO Diets and Digestive Health – It’s about Fermentable Carbohydrates

SIBO Treatment: Antibiotics or Diet?