Naturopathic Treatment for Small Intestinal Bacterial Overgrowth (SIBO)

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Naturopathic Treatment for Small Intestinal Bacterial Overgrowth (SIBO)

Irritable bowel syndrome (IBS) is an extremely common functional digestive disorder that is notoriously difficult to treat due to its functional nature. Although IBS is a widely diagnosed condition, it is often misunderstood, which is not ideal, as it is a condition that affects a huge chunk of the population, with some estimates as high as 28 percent. IBS is characterised by abdominal pain, flatulence, bloating, gas, abdominal discomfort, and changes in bowel habits (constipation and diarrhoea) and is diagnosed when other conditions with structural diagnostic criteria (such as IBD or celiac disease) have been ruled out. In other words, IBS is a “diagnosis of exclusion.”

Because the mainstream medical community currently has no defined cause of IBS, standard treatment is based primarily on symptom suppression, rather than treating the underlying cause. This may include antidiarrheal medications, anticholinergic or antispasmodic medications, laxatives, SSRIs, or 5-HT3 antagonists. These drugs primarily target intestinal motility and pain relief as a way to address a patient’s symptoms.

Furthermore, many of these drugs can cause unwanted and problematic side effects.

Fortunately, the research literature is starting to show strong evidence around the potential causes of IBS, allowing us to develop safer and more targeted treatments for IBS.

It is thought that one of the main causes of IBS is a condition called small intestinal bacterial overgrowth (SIBO). Diagnosis of SIBO has increased in recent years, particularly due to its very close association with irritable bowel syndrome (IBS).

While microbes are present throughout the gastrointestinal tract, a healthy small intestine contains relatively few microbes, especially compared to the large intestine. SIBO occurs when there is an excessive amount of bacteria in the small intestine and the bacterial population resembles that of the large intestine. This means there is an overgrowth of commensal bacteria in the small intestine. SIBO is defined as bacterial populations exceeding 10^5 – 10^6 organisms/ml. Usually there are less than 10^3 organisms in the small intestine. Most are gram positive bacteria, however SIBO involves the overgrowth of gram-negative species. These overgrown species produce various inflammatory molecules.

This creates inflammation in the small intestine walls, which decreases digestion and food/nutrient absorption, due to damage of the absorptive cells of the small intestine walls.

This results in undigested food staying in the small intestine and also moving into the large intestine where it is excessively fermented by bacteria to produce excessive gas, which is responsible for the symptoms of IBS such as bloating, reflux, stool issues (e.g. constipation and diarrhea), food intolerances and allergies (e.g. lactose, gluten, dairy, FODMAP, fructose) and abdominal discomfort/pain. The small intestine is where nutrient absorption occurs, therefore inflammation in the small intestine walls decrease nutrient absorption leading to nutrient deficiencies such as calcium, iron, magnesium, protein, zinc and vitamins A, D, E, K, omega 3’s, other fats and B12, which can create their own health issues such as anemia, peripheral neuropathy and osteoporosis. Correcting these nutritional deficiencies are vital to SIBO treatment.

Inflammation in the intestinal walls also decreases small intestine integrity. The small intestine is a semi permeable barrier that keeps out microbes and toxins from our food and water that we ingest, and allows nutrients to pass through its wall, into the bloodstream in order to provide nutrients for the body. It does this through the regulation of tight junctions in our gut wall. Tight junctions are like little gates in our gut wall that regulate what gets absorbed and what doesn’t. The millions of microbes that inhabit our digestive tract play an important role in keeping the integrity of the gut barrier by interacting with our tight junctions.

An imbalance of good and bad bacteria, as in SIBO, leads to inflammatory substances produced from bad bacteria, which can impair the integrity of the gut wall, causing it to become permeable (i.e. “leaky gut syndrome”). A leaky gut leads to large protein molecules, undigested food, bacteria and inflammatory molecules escaping into the bloodstream. Since these substances don’t belong outside of the gut (as a healthy gut should keep them out) and appear foreign to the immune system, the body mounts an immune response and attacks them. This can cause allergic reactions to certain foods. 

The bacteria that inhabit our guts also play a large role in regulating our immune function as 80% of immune cells are located in our gut. An unhealthy microbiome will cause disruptions to the immune system, which can lead to food allergies, where the body ultimately mounts immune responses on harmless proteins that are located in our food. However, they are perceived as harmful by the body due to disruptions in the immune system. 

Allergies to food can manifest in uncomfortable digestive symptoms, as well as exacerbate other health problems such as skin issues, hormonal imbalances and even mental health issues. The systemic immune response leads to low-grade, chronic inflammation in the body, which is the underlying driver of many chronic health conditions today.

Chronic inflammation in the body causes dysfunction and damage to other tissues and organs systems, which is also why IBS is linked to many other chronic health issues and inflammatory conditions.

It must also be noted that while the research on SIBO is growing rapidly, there is still a lot we don’t know. Some researchers hypothesize that there are different types of SIBO, with different types of bacteria that overgrow in various locations within the small bowel. These different types of SIBO may be correlated with specific conditions (e.g. one type of SIBO may be responsible for fibromyalgia).

The number of people with SIBO in the general population remains unknown. Some studies suggest that between 6 to 15% of healthy, asymptomatic people have SIBO, while up to 80% of people with irritable bowel syndrome (IBS) have SIBO.

Despite the numbers quoted above, SIBO is largely under-diagnosed and the prevalence is not fully understood. This is because many people don’t seek medical care for their SIBO symptoms, and because many doctors aren’t aware of how common SIBO is. Complicating this, the most commonly used tests to diagnose SIBO have various methodological issues.

What causes SIBO, how is it diagnosed and how is it treated?

One of the main causes of SIBO are thought to be altered intestinal motility. This is where the normal cleansing wave of the small intestine is disrupted, or stopped. This cleansing wave is called the Migrating Motor Complex (MMC), and occurs approximately every 90 minutes, typically between meals. The function of the MMC is to wash out accumulated bacteria and propel them toward the colon. Disrupted MMC function leads to bacterial stasis, which means that bacteria are allowed to grow throughout the small intestine. Dysfunctions in the MMC can be due to increased alcohol consumption (which causes inflammation in the gut), high blood glucose levels/diabetes (which cause neuropathy to the MMC), stress and over-use of pharmaceuticals that impair GIT motility (i.e. beta-blockers, narcotics, calcium channel blockers and opiate drugs).

However, dysfunctions in the MMC are most commonly a result of gut infections from parasites or bacteria that may been picked up while travelling or from food poisoning (i.e. post infectious gastroenteritis), There are 4 main infectious organisms responsible for post infection SIBO: Campylorbacter jejumi, E.coli, salmonella and shignella. The inflammation resulting from these infections causes damage to the neurons of the MMC, which is why some people can develop SIBO after a bad bout of food poisoning or gastroenteritis.

Once SIBO occurs, the overgrown bacteria and resulting inflammation further damages the MMC. Another main driver of SIBO is decreased stomach acid production as a result of stress, ageing and overuse of ant-acid drugs (e.g. nexium) for reflux. This is because stomach acid kills “bad” bacteria before it can move into the small intestine.

Another main driver of SIBO is decreased stomach acid production as a result of stress, ageing and overuse of ant-acid drugs (e.g. nexium) for reflux. This is because stomach acid kills “bad” bacteria before it can move into the small intestine.

Lastly, overuse of antibiotics (as it imbalances the gut flora), poor diet habits (e.g. lack of fibre from fruit and veggies and high processed carb intake), ageing, alcohol consumption, long term use of drugs such as immunosuppressant and the contraceptive pill, lack of sleep, lack of exercise, stress, altered intestinal anatomy and initial colonization of bad bacteria via caesarean birth/lack of breastfeeding, can all be driving factors behind SIBO. This is because all of these factors, through various mechanisms, can cause imbalances to the gut mirco-biome, as well as affect the MMC and decrease the gut’s immune defences to prevent overgrowth. This is through various mechanisms, which revolve around damaging the MMC, increasing inflammation in the gut and altering the composition of bacteria in the gut.


Testing for SIBO in clinical practice is usually done via a non-invasive breath test. After a 24 hour preparatory diet, a lactulose preparation is swallowed.

Lactulose is not absorbed and therefore acts as a food source for bacteria to ferment, if present, in the small intestine.

The bacteria ferment the lactulose and produce hydrogen and/or methane. These are diffused into the bloodstream and exhaled via the breath. High levels of both gasses are associated with SIBO. Methane is more closely related to constipation predominant IBS and hydrogen with diarrhoea predominant. 

Methane and hydrogen cause further inflammation in the gut walls and damages the MMC.

It must be noted that the breath test for SIBO does carry some methodical issues that can lead to false positives and false negatives. Therefore, test results must be interpreted with these methodical issues in mind.  


The treatment of SIBO is complex and multifaceted and should be done under the guidance of an experienced practitioner. It involves diet and lifestyle changes, removing drivers of the condition, as well as evidence-based herbal/nutritional supplementation to decrease symptoms, replete deficient nutrients, address inflammation, increase gut motility (MMC) and most importantly, clear the bacterial overgrowth in the small intestine. Herbal antimicrobials and/or locally acting antibiotics are typically used to get rid of the overgrown bacteria in the small intestine.

Lastly, natural and pharmaceutical prokinetics (motility agents) are used to help stimulate the MMC that may have been damaged. This is to prevent relapse, as relapse rates are very high in SIBO patients after antimicrobial treatment, due to dysfunctions in the MMC.

If you think that you may be suffering from SIBO, or have been diagnosed with IBS, call Oak Health today or book an appointment online to regain your guy health and get treated!  

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