SIBO, IBS, & the Low FODMAP Diet

 The symptom overlap between irritable bowel syndrome (IBS) and small intestinal bacterial overgrowth (SIBO) is quite extensive, but is the low FODMAP diet useful for both? This article highlights the latest available research to answer this through the following questions:

  • What is small intestinal bacterial overgrowth (SIBO)?
  • What are the similarities and differences between IBS and SIBO?
  • How common is SIBO in the IBS population?
  • Why do IBS and SIBO have similar symptoms?
  • Does SIBO cause IBS?
  • Is low FODMAP the best diet therapy for SIBO?

What is Small Intestinal Bacterial Overgrowth (SIBO)?

Briefly, SIBO stands for small intestinal bacterial overgrowth. The American College of Gastroenterology defines SIBO as an excessive microbial burden that resides in the small intestine, when those microbes should be residing in the colon. For that microbial burden to be classified as SIBO, it must be both measurable (via small bowel aspirate or breath testing) and associated with gastrointestinal symptoms, like bloating, abdominal pain, flatulence, constipation, or diarrhea.

 Note that there is a reason that we say it’s a “microbial” burden and not a “bacterial” burden. It was recently discovered that the methane dominant form of SIBO is not caused by bacteria at all. It is caused by a different type of microbe called methanogens, which belong to the Archaea kingdom. This discovery has led to reclassification of methane dominant SIBO to another term, called intestinal methanogen overgrowth (or IMO).

For the purposes of this article, when we refer to SIBO, note that we are referring to both SIBO and IMO. To get the full scoop on SIBO and IMO, including how they’re diagnosed and the different SIBO types and symptoms, check out our prior article SIBO: Get the Facts. The present article focuses on the overlap of SIBO, IBS, and application of the low FODMAP diet.


What are the similarities and differences between IBS and SIBO?

SIBO symptoms tend to mimic IBS symptoms. A 2020 research update outlines these well. Specifically, diarrhea associated with hydrogen and hydrogen-sulfide SIBO mimics IBS-D, while constipation associated with IMO mimics IBS-C. Dysmotility is a trademark of both. One study notes that as many as 60% of IBS-D patients also fulfill criteria for SIBO, and describes the presence of carbohydrate intolerance (lactose, fructans, fructose, oligosaccharides) in both conditions as well. Bloating, abdominal pain, flatulence, diarrhea, and constipation are all common symptoms among varying SIBO and IBS forms.

There are key differences to note as well. While SIBO is a measurable form of microbial imbalance that manifests in the small bowel, IBS is a functional bowel disorder with a wide variety of potential etiologies that is defined by abdominal pain for at least 1 day per week and change in stool form or frequency for at least 6 months prior to diagnosis. Notably, IBS is considered a diagnosis of exclusion after testing fails to identify an alternate diagnosis. While IBS is diagnosed as a syndrome (or a collection of symptoms) by testing for exclusion of other conditions, SIBO is diagnosed via breath testing, small bowel aspirate, or empiric treatment with antibiotics.

Compared to IBS, SIBO is also more likely to present with vitamin B12 deficiency (particularly in hydrogen dominant SIBO), iron deficiency, fat malabsorption, unintentional weight loss, and excessive gas production. Lastly, SIBO involving gram negative coliforms, like Klebsiella species, is more likely to cause villous atrophy compared to IBS, which, by definition, does not involve destructive inflammation of gastrointestinal tissues. 

How Common is SIBO in the IBS Population?

The long-and-short of it: it is common to develop SIBO when IBS is already present.

IBS is considered a risk factor for SIBO. One meta-analysis of 25 studies and over 6,000 subjects showed that 31% of patients diagnosed with IBS also tested positive for SIBO. Compared to controls without IBS, those with IBS were 3.7 times more likely to also test positive for SIBO. That same meta-analysis also compared SIBO prevalence in patients with IBS to healthy controls with no prior existing condition. Those with IBS were 4.9 times more likely to be diagnosed SIBO than non-IBS healthy controls (OR = 4.9; 95% CI 2.8-8.6).

Based on these findings, the overlap is quite significant, but an important factor to take into consideration here is that the strength of the existing evidence of this overlap remains relatively low. Though the studies outlined here are considered gold standard designs (systematic reviews and meta-analyses), the main limitations of the research are the diagnostic methods used for SIBO and IMO (i.e. breath testing). Until a more sensitive, specific, and non-invasive diagnostic tool is developed for SIBO, it will be difficult to truly quantify the proportion of IBS patients who develop SIBO.

Does SIBO Cause IBS?

Despite the overlap in symptomatology, SIBO is not considered to be a “cause” of IBS. The underlying etiology of IBS is complex and multifactorial, and SIBO is no different in this regard. SIBO is considered a secondary symptom that occurs as the result of something else, commonly a pre-existing condition or series of variables that results in small bowel dysmotility. For now, the literature points to IBS as a potential risk factor for the development of SIBO, among other variables, and not the other way around. However, because SIBO tends to manifest as an exacerbation of IBS symptoms, treatment and management of concurrent SIBO in IBS patients may result in clinically significant symptom improvement of both SIBO and IBS.

Why Do IBS and SIBO have Similar Symptoms? 

So, if SIBO doesn’t cause IBS, why are the symptoms so similar?

A current theory to explain their commonalities involves gut microbiome dysbiosis, which is a general term (and not a diagnosis) used to describe an imbalance of gut microbes along the digestive tract.

SIBO is one manifestation of dysbiosis that is linked to IBS symptoms, whereby harmless microbes that typically inhabit the colon reside and multiply in the small bowel instead. Among IBS patients, some studies have shown reduced bacterial abundance and diversity in the colon.  Disruptions in the colonic microbiome may subsequently contribute to dysmotility, visceral sensitivity, immune alterations, and changes in the gut-brain axis in IBS patients.

Patients with either (or both) IBS and SIBO are therefore considered more likely to experience dysmotility, intestinal permeability, autoimmunity, decreased bile acid absorption, chronic systemic inflammation, and altered mind-gut interactions that occur via the enteric nervous system due to differing forms of gut microbial dysbiosis. Altogether these alterations manifest in clinically similar symptoms, including bloating, abdominal pain, excessive flatulence, and alterations in bowel habits. More research is needed to confirm dysbiosis as the primary underlying connection, but it is one of the main theories being assessed at present. The specific microbiome alterations associated with SIBO and IBS is also a growing area of research with potential therapeutic implications in the future. So far, Enterococcus, Escherichia coli, and Klebsiella, and Methanobrevibacter smithii have been implicated. 

Is low FODMAP the best diet therapy for SIBO? 

Time for the burning question! Which diet should you trial if you have SIBO? There is quite a bit of buzz around this topic. Some names you may have heard include the specific carbohydrate (SCD) diet, SIBO specific diet, biphasic diet, the low fermentation diet, the elemental diet, and of course, low FODMAP. So, let’s outline some of the facts before we delve deeper into this:

  • Diet has not yet been formally studied for management of SIBO.
  • There is no singular evidence based “SIBO diet.”
  • Different SIBO types may necessitate different diet approaches.

Given these parameters, the absence of formalized evidence, and what we know in the literature to date regarding SIBO symptomatology, many leaders in the field still consider a modified low FODMAP approach to be the most scientifically sound and minimally restrictive diet approach for SIBO. Here is why. 

Recall that the majority of the low FODMAP literature uses IBS-D patients as the study population, and that up to 60% of those with IBS-D fulfill criteria for SIBO diagnosis. Although low FODMAP has not been studied for SIBO specifically, there is considerable overlap in the SIBO population and study populations previously assessed in IBS research. A strong body of literature has now amassed that shows between 50-86% efficacy of the low FODMAP diet for those with IBS. The overlap in study populations may suggest at least some applicability of the low FODMAP diet to the SIBO population – but again, this remains to be examined.

Carbohydrate intolerance has been noted in both IBS and SIBO patients. Most nutrition interventions for SIBO target carbohydrate intake. By limiting highly fermentable carbohydrates, the theory is that the microbes that have translocated into the small bowel in SIBO will lose their fuel source and will therefore produce less gas, resulting in fewer symptoms. Notably, this is not considered to “starve out” the translocated microbes, but instead to limit the symptoms they may cause via fermentation in the small bowel. Reducing certain carbohydrates may also reduce osmotic pressure in the small bowel, which can alleviate post-meal discomfort for SIBO patients with visceral hypersensitivity and FODMAP intolerance. 

Low FODMAP protocols confer benefits for people living with IBS by reducing gas production in the distal small bowel, osmotic pressure in the small bowel and colon, histamine release, and visceral sensation or pain. These are some of the underlying variables that may increase symptoms for those with SIBO, as well. Further, the low FODMAP protocol includes all food groups and is considered less restrictive than many other SIBO diet approaches, with varying approaches that allow for greater flexibility. Therefore, for SIBO cases in which symptoms are worsened by highly fermentable carbohydrate intake, a modified low FODMAP diet may confer similar benefits without excessive restriction. Certain low or moderate prebiotic fibers may also be incorporated to feed beneficial bacteria in the colon while treating to eradicate microbes in the small bowel. As with any case, application of the low FODMAP protocol for patients with SIBO should be screened for appropriateness and is best conducted under the supervision of a GI-specialized dietitian to ensure nutritional adequacy and troubleshoot challenges.

Of note, the SCD and low fermentation diet also limit intake of highly fermentable carbohydrates, but the differences between these approaches and the low FODMAP diet is important. The SCD, for example, limits carbohydrates that require disaccharidases for digestion, like lactose, starch, and sucrose. However, it allows foods with excess fructose, like honey. Though these carbs do not require disaccharidases, we now know that excess fructose is malabsorbed in the small bowel is as many as 1 in 3 people and may worsen symptoms for those with SIBO. The low fermentation diet, by contrast, does limit foods with fructose in excess of sucrose and some fermentable carbohydrates, but allows others like onion, garlic, and wheat-containing pastas, which may elicit symptoms.

Though these diets have their merits and may be useful on a case-by-case basis, they also contain some variations regarding permissible carbohydrates and supportive research in the IBS population, which are two strengths of the low FODMAP diet. Some are also considered to be highly restrictive, increasing risk of nutritional inadequacy and food hyper-vigilance without appropriate clinical supervision.


Many practitioners eagerly await emerging evidence on the best diet approach (or approaches) for SIBO. Though the low FODMAP diet remains to be formally studied in the context of SIBO, there is a relatively stronger scientific basis for its application in SIBO compared to the abovementioned diets, particularly for those with IBS. It may be tempting to consider the points outlined in this article as “evidence” in favor of the low FODMAP diet for SIBO, but recall that we cannot consider low FODMAP an “evidence-based” diet approach for SIBO until there are high quality studies conducted on this subject, within this specific patient population. There is currently one under way at a renowned hospital in Boston. For now, however, the low FODMAP diet is considered a scientifically plausible diet approach to mitigate symptoms of SIBO after treatment. Dietary approaches utilized in the management of SIBO at present involve symptom mitigation, but as research evolves, there will likely be differing dietary approaches to SIBO management depending on the types of gas and microbes overgrowing in the small bowel.

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