Small Intestinal Bacterial Overgrowth (SIBO) – An Explanation for IBS

Small Intestinal Bacterial Overgrowth (SIBO)

Do you suffer from digestive issues like gas, bloating, cramping, abdominal pain/discomfort, stool issues (e.g. constipation/diarrhoea) and reflux? Do you suffer from allergies and food intolerances? Do you suffer from a chronic health condition? Have you been diagnosed with Irritable Bowel Syndrome (IBS)?

If you answered yes to these questions, you might be suffering from a condition called SIBO (small intestinal bacterial overgrowth). It is thought to be one of the main underlying drivers of IBS symptoms and can help provide long time suffers of IBS with a physiological explanation to their uncomfortable symptoms.

Small intestinal bacterial overgrowth, an underlying cause for Irritable Bowel Syndrome (IBS).

“All disease begins in the gut.”

– Hippocrates

Hippocrates said this more than 2,000 years ago, but we’re only now coming to understand just how right he was. In fact, many researchers believe that supporting intestinal health and restoring the integrity of the gut barrier will be one of the most important goals of medicine in the 21st century.

Research over the past two decades has revealed that gut health is extremely critical to overall health, and that an unhealthy gut contributes to (even causes) a wide range of modern diseases and disorders that we see today.

In simplistic terms, within the gut, there is both “good” and “bad” bacteria. The “good” bacteria is obviously health promoting and the “bad” (in excessive amounts) is not. The good bacteria keep the bad in check. If the bad are allowed to flourish and overrun the good (i.e. overgrowth) then they start to cause issues. In the gut, it is all about balance.

People with chronic diseases have been shown to have a significantly different composition of gut bacteria when compared to healthy individuals, which demonstrates how gut composition plays a large role in the development of diseases.

What is SIBO and how does it relate to Irritable bowel syndrome (IBS)?

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 characterized by abdominal pain, flatulence, bloating, gas, abdominal discomfort, and changes in bowel habits (constipation/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, which will be outlined in this blog series.

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 is less than 10^3 organisms in the small intestine. Most are gram positive bacteria, however SIBO involves the overgrowth of gram negative species. Typical species that overgrow in the small intestine are Klibsiella pnemonae, E.coli, Strep spp., Staph spp., Proteus spp., Bacterioides spp., Clostridium spp., Micrococcus, and Enterroccocus spp. These overgrown species produce various inflammatory molecules.

This creates inflammation in the small intestine walls, which decreases brush border enzyme production (digestion) and decreases nutrient absorption, due to damage of the abortive cells of the small intestine. 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 gas, which is responsible for the symptoms of IBS such as bloating, reflux, stool issues, food intolerances/allergies (e.g. lactose, 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 blood stream 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 are foreign substances to the immune system, the body mounts an immune response and attacks them. This can cause allergic reactions to certain foods.

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 as an underlying cause such as:

  • Fibromyalgia and Chronic Fatigue Syndrome – especially associated with diarrhoea dominant SIBO
  • Chronic constipation – associated with methane-dominant SIBO
  • Irritable bowel syndrome (IBS)
  • Inflammatory Bowel disease (Crohn’s disease and ulcerative colitis)
  • Acid reflux
  • Coeliac disease
  • Interstitial Cystitis
  • Restless leg syndrome
  • Acne Rosacea
  • Diabetes
  • Hypothyroidism
  • Scleroderma
  • Chronic Prostatitis
  • Non-Alcoholic Steatohepatosis (NASH)
  • Liver cirrhosis
  • Joint pain
  • Diverticulitis
  • Depression and anxiety
  • CVD
  • Allergies and intolerances
  • Chronic kidney disease
  • Chronic pancreatitis
  • Endometriosis (due to the adhesions that can occur on the small intestine walls, which effects the MMC)

 Because SIBO is a large underlying driver of these above conditions, treating SIBO will be essential to managing these conditions, as it will reduce the underlying cause. 

 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 over-use 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 immune suppressant and the contraceptive pill, lack of sleep, lack of exersize, stress, altered intestinal anatomy and initial colonization of bad bacteria via caesarean birth/lack of breast feeding, 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 effect the MMC complex and decrease the guts 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.


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 anti-microbials 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 anti-microbial 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 a consult online to find out how practical diet and lifestyle interventions, as well as herbal and nutritional supplementation can help improve your symptoms and overall well being. 

You may also be interested in the 6 week gut healing program.