Skip to content
Small intestinal bacterial overgrowth is increasingly recognised as a cause of abdominal bloating, pain and diarrhoea. Historically believed to afflict only those who had structural abnormalities of the gastrointestinal tract1, it is actually an increasingly common cause of digestive symptoms: up to 78% of individuals with irritable bowel syndrome, one of the most widespread gastrointestinal complaints worldwide, have been found to have SIBO on breath testing.2
In this article we will cover:
Small Intestinal Bacterial Overgrowth, or SIBO, is the excessive growth of bacteria in the small intestine. The small intestine usually is colonised by some bacteria but much less than the large intestine. When there is an abnormally high quantity of bacteria in the small intestine, there is increased bacterial fermentation of food as it enters from the stomach. This results in increased gas production, usually hydrogen and sometimes methane gases. Those with predominantly hydrogen-producing bacteria typically suffer from diarrhoea, SIBO-D, and those with predominantly methane-producing bacteria may experience constipation symptoms, SIBO-C. As high hydrogen levels can also indicate lactose intolerance, it is important to determine the underlying cause of your symptoms.
In the short term, increased gas production can lead to bloating, flatulence, nausea and abdominal pain. Long term, bacterial overgrowth can lead to local intestinal mucosal inflammation. This can damage the lining of the intestinal tract, flattening villi and thinning the mucosa which can in turn, prevent optimal absorption of nutrients, in some cases leading to vitamin and mineral deficiencies.
SIBO can have a number of causes, and it is important to understand the cause to be able to choose the most appropriate treatment. The causes can be:
The two most common causes of SIBO are reduced gastric acid secretion and impaired small intestinal motility3. Stomach acid inhibits the growth of bacteria that is ingested in our food. Normal intestinal motility keeps the contents of our small intestine moving and prevents stasis of food and bacteria, which can lead to bacterial overgrowth.
Recurrent or long-term antibiotic use is also a risk factor for the development of SIBO. Antibiotics can alter the composition of bacteria in the small intestine leading to increased growth of pathogenic bacteria. For more about antibiotics and the microbiome, take a look at this article in the Probiotics Learning Lab: Probiotics and Antibiotics.
Poor function of the the ileocaecal valve, located at the junction between the ileum (small intestine) and the caecum (start of the large intestine), is also a risk factor for SIBO. This valve prevents the “backflow” of colonic contents from re-entering the small intestine, but individuals with a dysfunctional ileocaecal valve are at increased risk of developing SIBO as colonic bacteria can enter and colonise the small intestine more easily4.
Individuals with immune deficiencies, such as with HIV, are also prone to bacterial overgrowth.
Symptoms of SIBO may be related to the underlying cause of SIBO (low stomach acid, poor motility), the manifestation of SIBO itself, or the consequences of malabsorption. SIBO-C, typically associated with higher methane producing bacteria, presents with constipation whereas SIBO-D, typically associated with hydrogen producing bacteria, presents with diarrhoea but other common symptoms include:
Signs of corresponding malabsorption could include:
SIBO is typically diagnosed based on patient history, followed by a diagnostic test. Healthy individuals have less than 103 CFU (or colony forming units) of bacteria per millilitre of digestive fluid in the small intestine. There are currently two diagnostic tests used for SIBO:
SIBO can be diagnosed when there is greater than 103 CFU of bacteria cultured per mL of digestive fluids from the small intestine. This aspiration can be performed on endoscopy, but it is not routinely practised as it is time consuming and expensive, and is an invasive procedure with some risk attached to performing it.
Hydrogen gas is produced by bacteria in the gastrointestinal tract as a by-product of fermentation of simple carbohydrates. During this diagnostic test, glucose or another simple carbohydrate is given to a patient, and the hydrogen and methane* gases exhaled in their breath over the following 90 minutes, is measured. This is under the premise that hydrogen is rapidly produced by bacterial fermentation in the small intestine. The gases are absorbed into the bloodstream and excreted in the breath. A rise of 20ppm in exhaled hydrogen above baseline within 90 minutes of oral ingestion of 75g of glucose is considered diagnostic. There are many benefits with this type of testing including its wide availability, it is inexpensive, non-invasive and technically easy to perform. However, there is an increased risk of false positives as some individuals have faster colonic transit, and hydrogen may be produced in the colon. It is also relatively poor at diagnosing SIBO in the distal small intestine (the furthest end of the small intestine) as glucose is absorbed proximally (in the nearest end). Meaning that the glucose may not reach the distal small intestine and trigger bacterial fermentation here.
*Human cells are incapable of producing hydrogen and methane gases. Although methane is not produced by bacteria, the archaea that produce it use hydrogen as a substrate so its presence suggests increased hydrogen production. A rise of greater than 10 ppm of methane is diagnostic of methanogenic archaea overgrowth.
There are three areas to address when managing SIBO:
As discussed above, there are various underlying causes of SIBO. Medication use can be reviewed and potentially stopped, such as proton pump inhibitors and opiates, under the guidance of a healthcare practitioner. Avoiding fermentable carbohydrates such as in the low FODMAP diet can reduce bacterial fermentation in SIBO and could be considered, again under the guidance of a healthcare practitioner6. Managing IBS requires an individualised approach - you can read more about this in our article on remedies for IBS.
Addressing nutritional deficiencies is very important. Vitamin B12 and fat-soluble vitamins A, D, E and K may need to be supplemented. Damage to the lining of the intestinal tract can also prevent enzyme production which may require supplementation with digestive enzymes3.
Although there is no universally accepted standardised treatment for SIBO, the mainstay of treatment of SIBO currently is with antibiotics to reduce bacterial colonisation in the small intestine5. R*******n is the best studied antibiotic for this purpose as it has poor systemic bioavailability which means that it mostly works locally in the gastrointestinal tract7. The British Society of Gastroenterology use 550mg of r*******n twice daily for 7 days in those with abnormal breath tests8. Often SIBO returns and more antibiotics are needed, this alongside increased knowledge of the consequences of overuse of antibiotics have seen the adoption of a more cautious approach with antibiotics.
Naturopathic protocols for SIBO include changes to diet, adopting a low-FODMAP diet in many cases, probiotics, herbal anti microbials and lifestyle changes. The most common approach is known as the ‘Five R’s’ protocol and at the appropriate stage, probiotics can be introduced.
Saccharomyces boulardii has a number of modes of action that can be helpful in SIBO. As part of a 'Five R's' protocol, its antimicrobial properties can be used to inhibit the growth of pathogenic bacteria and remove them from the gut whilst soothing an inflamed gut by restoring levels of SCFA’s and stimulating the production of anti-inflammatory molecules14. Soil based probiotics have been shown to reduce symptoms of SIBO and prevent it from coming back which is a common occurrence, although further research is needed, one hypothesis is that it is because they don’t colonise in the small intestine and possess anti-inflammatory properties10.
As healthcare professionals we get asked a wide variety of questions about SIBO. The main question being, are probiotics bad for SIBO? Or, conversely, which probiotic is best for SIBO? And more recently, a new question, which are the best soil based probiotics for SIBO. Let’s look at the best probiotic strains for SIBO.
Although it may be seen as contradictory to use probiotics in small intestinal bacterial overgrowth, one particular probiotic yeast, Saccharomyces boulardii, which is a probiotic yeast, and soil-based probiotics have been identified as beneficial. Let’s look at how Saccharomyces boulardii and soil based probiotics might help with SIBO. Could either of these be the best probiotic for SIBO?
As a yeast, Saccharomyces boulardii can be taken alongside antibiotics and its functioning is unaffected. It has known anti-inflammatory effects in the gut9 and can inactivate pathogenic toxins10 and stimulate enterocyte (cells of the intestinal lining) maturation11.
In a pilot clinical study of 40 patients diagnosed with SIBO due to the autoimmune condition, systemic sclerosis, the effects of Saccharomyces boulardii on hydrogen production and SIBO eradication was assessed and compared with m***********e, a common antibiotic used in the treatment of SIBO12. The patients were divided into 3 groups; one group were given m***********e alone for 1 week, another group were given m***********e with Saccharomyces boulardii for 1 week and the third group were given Saccharomyces boulardii alone for 1 week. Two months later, hydrogen breath tests were repeated. The group that achieved the best results was the m***********e and Saccharomyces boulardii group, with SIBO eradicated in 55% of participants at 2 months. Saccharomyces boulardii therapy alone eradicated 33% which was better than the group given m***********e alone (with just 25% SIBO eradication). Of note, the Saccharomyces boulardii group had the lowest level of adverse effects from treatment, and taking SB alongside m***********e appeared to reduce the risk of antibiotic side-effects from 53% to 36%12. The results of this clinical study suggest Saccharomyces boulardii as a potential beneficial adjunct to antibiotic therapy when treating SIBO.
Interestingly, soil based probiotics have shown promise in SIBO. A small gold standard trial investigated B. coagulans Unique IS-2 in 30 individuals with chronic abdominal pain or diarrhoea and a positive hydrogen breath test (HBT), SIBO-D. All participants underwent three weeks of antibiotic therapy (using broad spectrum antibiotics). The individuals were then randomised to receive either B. coagulans Unique IS-2 or a placebo daily for 15 days alongside a maintenance antibiotic dose. After six months, GI symptoms and HBT’s were analysed. In the probiotic group, GI symptoms including belching, flatulence and diarrhoea had all significantly improved and abdominal pain had disappeared completely. HBT’s turned negative in 93% of individuals in the probiotic group compared with 67% in the placebo group13
If you liked this article, read more about the research behind Saccharomyces boulardii over on our Probiotics Database.