Treating SIBO Naturally


Do you suffer from bloating, gas, diarrhoea or constipation?

So often these symptoms are labelled as IBS (Irritable Bowel Syndrome) and you walk away from your appointment with your doctor with little understanding of what is actually causing your symptoms and what you can do to address them.

Whilst IBS is more and more common these days, 70% of IBS cases are actually SIBO and a lot of these are frequently missed by health professionals due to the similarities in symptoms. 

What is SIBO?

In short, SIBO is small intestinal bacterial overgrowth.

Our gut is made up of trillions of different types of bacteria, and other micro-organisms called our microbiome. These bacteria are vital to our health and wellbeing and work synergistically in the gut to produce metabolites which are used throughout the body for things like digestion, energy, immune function, mood regulation, sleep and hormone activity.

In a healthy gut, the majority of the bacteria is found in the large intestine. Small Intestinal Bacterial Overgrowth (SIBO) is the term used when the bacteria in the large intestine proliferate into the small intestine. It’s not an infection and doesn’t involve pathogenic bacteria – it involves bacteria that are supposed to live in the large intestine. This causes food to ferment higher up in the digestive tract which leads to symptoms such as bloating, gas and diarrhoea. The symptoms are caused by the overgrowth of bacteria fermenting particular foods into gases.

Symptoms of SIBO include:

  • Bloating
  • Excessive gas
  • Diarrhoea
  • Constipation
  • Abdominal pain and cramping
  • Feeling full after eating only a small amount
  • Burping
  • Reflux
  • Nausea and vomiting
  • Weight loss
  • Food intolerances and sensitivities
  • Brain fog
  • Low moods
  • Fatigue
  • Skin issues such as eczema and rosacea
  • Nutrient deficiencies
Symptoms of SIBO include bloating, excessive gas, diarrhoea, constipation, abdominal pain and cramping, and more

Causes and Risk Factors

SIBO develops when certain normal mechanisms that control the bacterial populations are disrupted. The two main processes that predispose an individual to bacterial overgrowth include low gastric acid secretion and small intestine motility dysfunction.1

  • Low Gastric Acid 

Gastric acid suppresses the growth of ingested bacteria and therefore reduces bacterial count in the upper small intestine. If someone isn’t producing enough gastric acid, this can lead to proliferation of bacteria in the small intestine. Low gastric acid secretion can develop after colonization with Helicobacter pylori infection or as a consequence of ageing.

  • Motility Disorders

Certain motility disorders which can affect the movement of food throughout the gastrointestinal system can lead to SIBO. For example, gastroparesis, a chronic disorder of delayed gastric emptying which can develop secondary to diabetes, connective tissue disorders, viral infection and ischemia can lead to SIBO due to food and bacteria staying too long in the upper small intestine.2 Other disorders include Celiac disease, cirrhosis, chronic renal failure, scleroderma and portal hypertension can predispose someone to developing SIBO as bacteria may not be effectively swept from the proximal bowel to the colon.

  • Structural Abnormalities

Structural abnormalities in the gastrointestinal tract can also lead to SIBO as they provide an ideal environment for bacterial colonization and overgrowth. Certain surgeries and patients who have undergone jejunoileal bypass or the creation of a distal ileal pouch are also at risk of developing SIBO.

  • Immune function deficiency

People who are immunodeficient are also prone to bacterial overgrowth.3 This could be due to an abnormal antibody or T-cell response.

The main risk factors for SIBO include:

  • Irritable bowel syndrome or other digestive diseases like Celiac Disease and Inflammatory Bowel Disease (Crohn’s and Ulcerative Colitis)
  • History of antibiotic use
  • Any episode of food poisoning
  • Period of high stress
  • Low levels of stomach acid
  • Pancreatic insufficiency
  • Chronic alcohol use
  • Drugs, such as opiates
  • Proton pump inhibitors and immunosuppressant medications
  • Removal of the ileo-caecal valve
  • Any disease that slows functioning of the digestive system i.e. Diabetes, Hypothyroidism
  • Ageing due to medication use that slows gastrointestinal motility, dietary changes that lead to malnutrition, decline in mobility, decline in gastric acid production and changes in gut immune function

How is SIBO best diagnosed? 

There are a number of different ways to test for SIBO.  

  • Breath test

A breath test is the most common and accessible way.4 The bacteria that cause SIBO release gases of hydrogen and methane which can be measured through the breath test. Breath testing is non-invasive, relatively affordable and can be done at home. There is however currently no standard methodology for breath testing.5 Diagnosis of SIBO is really important as it will determine your most appropriate treatment protocol. Before doing the breath test, it is important to avoid antibiotics for four weeks and pro-motility agents and laxatives for at least one week before. Also, a strict bland diet, including avoidance of fermentable foods such as complex carbohydrates is recommended for the day before completing the test. Patients are also recommended to fast 8-12 hours before the breath test, to avoid smoking the day of the breath test and to minimise physical exertion during the breath test.6  

  • Bacterial culture

Bacterial culture is another way although it is seldom used due to its invasiveness, potential for contamination, cost, inaccurate sampling and because many bacterial species do not grow in routine culture and quantitative culture may underestimate the bacterial population. Furthermore, due to the location of the small intestine, it is not easily accessible to obtain a sample.

  • D-xylose test

D-xylose test is another method and this involves having a patient drink a certain quantity of D-xylose and measure the levels in the urine and bloods. If there is no evidence of D-xylose in the urine and blood, it suggests that the small bowel is not absorbing properly which is often an indicator for SIBO. Blood tests and case history are also important. 

There are a number of different ways to test for SIBO including Breath test, Bacterial culture and D-xylose test

Conventional Treatment for SIBO

SIBO is usually treated with a course of antibiotics. A variety of antibiotics including neomycin, rifaximin, amoxicillin-clavulanate, fluoroquinolone and tetracycline have been used, however, the best evidence is for the use of norfloxacin and amoxicillin-clavulanate.

Over the past decade, individuals with IBS and/or SIBO have been increasingly turning to complementary and alternative medicine options for symptom relief and disease management.7

Natural Treatment for SIBO

Natural treatment of SIBO is centred around correcting the underlying root cause of the bacterial overgrowth, eradicating the harmful bacteria whilst providing nutritional support, particularly for those patients who have lost weight or are deficient in vitamins and minerals.  

Dietary and Lifestyle Changes 

Diet alone is almost never enough to clear SIBO completely, but it is a vital part of the treatment nonetheless. It is important to firstly identify specific food irritants that you may be reacting to by undergoing either an Elimination Diet, Low FODMAP diet or Gluten Free/Dairy Free diet. Many people will see a significant reduction in their symptoms when eliminating gluten-containing foods in their diets and many also notice significant improvement when removing dairy from their diet due to lactose and casein sensitivity.

Another diet which is effective in eradicating SIBO is the Elemental Diet. This is usually reserved for patients who have relapsed or who have not seen results with the standard SIBO treatment as it is very strict, can be psychologically taxing and isn’t suitable for people who are quite unwell.

Some other simple dietary principles you can employ include: 

  • Focus on fresh, whole foods to make sure you’re getting your nutrients that are essential for healthy immune function  
  • Avoid sugar, sweets, soft drinks, fruit juices and alcohol as sugar encourages bacterial overgrowth  
  • Foods should be cooked and easy to digest to minimise fermentable material in the gut 
  • Consume protein at each meal to help balance your blood sugar levels and provide enough energy  
  • Avoid drinking with meals as this can dilute your stomach acid levels and digestive enzymes. It’s best to flush your body with one litre of water when you first get up as this can help to clear your digestive tract when your digestive system is at its emptiest  
  • Don’t eat your meals too close together to help you digest your food better  
  • Avoid or minimise stress as much as possible as this reduces immune activity and increases inflammation  
  • Focus on omega-3 rich foods including avocadoes, olive oil, flaxseed oil, hemp seed oil, walnuts, chia seeds and flaxseeds. Omega-3 fatty acids to reduce inflammation that may result from irritation in the gut.  


Nutritional support, particularly for those who have lost weight or have vitamin and mineral deficiencies is essential to SIBO treatment.8 Look at supplementing and maintaining your vitamin B12, vitamin A, D, E and K, as well as correcting any calcium, iron, zinc and magnesium deficiencies.

Partially Hydrolyzed Guar Gum (PHGG) is another good nutritional. This is a low cost prebiotic powder that you can add to your smoothies that promotes the growth of beneficial bacteria in the gut and works effectively to regulate bowel motions. It has also been found in the research to improve the effectiveness of rifaximin in SIBO treatment.

Using probiotics may seem counter-intuitive in SIBO and research is controversial on its effectiveness. Particular strains however have effects that are beneficial for SIBO such as motility enhancement, reduction of methane gas and abdominal hypersensitivity. A 2017 meta-analysis of 18 studies reported that probiotics were associated with significantly increased clearance of SIBO compared with non-probiotic therapy although probiotics were not found to be effective for the prevention of SIBO.9

Herbal Remedies

There are many great herbs that are antibacterial and antimicrobial and work well to eradicate SIBO. In fact, studies have shown that herbal therapy may be as effective as antibiotic therapy in the treatment of SIBO.10 Some of the common herbs used include:

  • Phellodendron

Phellodendron is traditionally used in Traditional Chinese Medicine to maintain upper intestinal health. It contains a number of constituents that is antimicrobial in nature. They help to block the adhesion of bacteria to the cells on the gut wall.

  • Oil of Oregano

Oil of oregano directly kills or strongly inhibits the growth of intestinal microbes.

  • Barberine

Berberine extracts are well known for their broad antibacterial activities.11 Some examples of Berberine containing herbs include Golden Seal, Oregon Grape and Barberry.

  • Thyme and Wormwood

Both these herbs have significant antimicrobial and anti-inflammatory properties that are important to the pathogenesis of SIBO.12

  • Allicin

Though Allicin is derived from garlic, it doesn’t contain the FODMAPs found in other parts of the clove. Allicin is a strong antimicrobial with Allimax as its highest potency formula. This has been found to be effective for methane-dominant SIBO. It often used in combination with Berberine.

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Dukowicz, A. C., Lacy, B. E., & Levine, G. M. (2007). Small intestinal bacterial overgrowth: a comprehensive review. Gastroenterology & hepatology, 3(2), 112–122

2 Dukowicz, A. C., Lacy, B. E., & Levine, G. M. (2007). Small intestinal bacterial overgrowth: a comprehensive review. Gastroenterology & hepatology, 3(2), 112–122

Pignata, C., Budillon, G., Monaco, G., Nani, E., Cuomo, R., Parrilli, G., & Ciccimarra, F. (1990). Jejunal bacterial overgrowth and intestinal permeability in children with immunodeficiency syndromes. Gut, 31(8), 879–882.

Rao, S., & Bhagatwala, J. (2019). Small Intestinal Bacterial Overgrowth: Clinical Features and Therapeutic Management. Clinical and translational gastroenterology, 10(10), e00078.  

Rezaie, A., Buresi, M., Lembo, A., Lin, H., McCallum, R., Rao, S., Schmulson, M., Valdovinos, M., Zakko, S., & Pimentel, M. (2017). Hydrogen and Methane-Based Breath Testing in Gastrointestinal Disorders: The North American Consensus. The American journal of gastroenterology, 112(5), 775–784.

Rezaie, A., Buresi, M., Lembo, A., Lin, H., McCallum, R., Rao, S., Schmulson, M., Valdovinos, M., Zakko, S., & Pimentel, M. (2017). Hydrogen and Methane-Based Breath Testing in Gastrointestinal Disorders: The North American Consensus. The American journal of gastroenterology, 112(5), 775–784.

Kong, S. C., Hurlstone, D. P., Pocock, C. Y., Walkington, L. A., Farquharson, N. R., Bramble, M. G., McAlindon, M. E., & Sanders, D. S. (2005). The Incidence of self-prescribed oral complementary and alternative medicine use by patients with gastrointestinal diseases. Journal of clinical gastroenterology, 39(2), 138–141

Dukowicz, A. C., Lacy, B. E., & Levine, G. M. (2007). Small intestinal bacterial overgrowth: a comprehensive review. Gastroenterology & hepatology, 3(2), 112–122

9 Zhong, C., Qu, C., Wang, B., Liang, S., & Zeng, B. (2017). Probiotics for Preventing and Treating Small Intestinal Bacterial Overgrowth: A Meta-Analysis and Systematic Review of Current Evidence. Journal of clinical gastroenterology, 51(4), 300–311.

10 Chedid, V., Dhalla, S., Clarke, J. O., Roland, B. C., Dunbar, K. B., Koh, J., Justino, E., Tomakin, E., & Mullin, G. E. (2014). Herbal therapy is equivalent to rifaximin for the treatment of small intestinal bacterial overgrowth. Global advances in health and medicine, 3(3), 16–24.

11 Han, J., Lin, H., & Huang, W. (2011). Modulating gut microbiota as an anti-diabetic mechanism of berberine. Medical science monitor : international medical journal of experimental and clinical research, 17(7), RA164–RA167.

12 Ogbolu, D. O., Oni, A. A., Daini, O. A., & Oloko, A. P. (2007). In vitro antimicrobial properties of coconut oil on Candida species in Ibadan, Nigeria. Journal of medicinal food, 10(2), 384–387.

13 Juteau, F., Jerkovic, I., Masotti, V., Milos, M., Mastelic, J., Bessière, J. M., & Viano, J. (2003). Composition and antimicrobial activity of the essential oil of Artemisia absinthium from Croatia and France. Planta medica, 69(2), 158–161.

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