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Small Intestinal Bacterial Overgrowth (SIBO)

Small Intestinal Bacterial Overgrowth (SIBO): A Functional Medicine Approach

SIBO is a complex gastro-intestinal disorder characterized by excessive bacterial growth in the small intestine. Unlike the large intestine, which hosts a diverse microbial community, the small intestine typically contains a low bacterial load.

For most chronic disorders Functional Medicine provides a more complete solution as it sees the body as one whole organism. This enables us to better understand the patient’s complete situation and thus how we can address root causes rather than focusing on symptom-relief.

Symptoms of SIBO

  • Bloating and abdominal discomfort due to increased bacterial fermentation.
  • Diarrhea and/or constipation caused by bacterial interference with normal digestion and absorption leading to altered bowel movements.
  • Abdominal pain and cramps due to inflammation.
  • Gas and belching from gas produced as a by-product from bacterial metabolism.
  • Nausea and vomiting: Irritation and inflammation of the gut lining can lead to nausea.
  • Malabsorption causing weight loss
  • Nutrient deficiencies from malabsorption.


Causes of SIBO

Usually, multiple factors would play a role in the development of SIBO and the importance of each factor may vary significantly from patient to patient. Some relevant contributors to the development of SIBO are as follows:

  • Prolonged intestinal transit can facilitate bacterial overgrowth.
  • Low stomach acid reduces or prevents the sterilization of the food which allows more bacteria to survive and reach the small intestine.
  • Impaired motility: Conditions like diabetes (diabetic gastroparesis) and scleroderma can affect the gut’s muscular activity and increase the intestinal transit time
  • Various medications can affect gut health and lead to the development of SIBO through different mechanism
    • Proton pump inhibitors and antacids: Reduces stomach acidity
    • Opioids: Can increase transit time
    • Bacteria: Can alter bacterial flora in the gut
  • Immunosuppressants can affect the gut microbiota
  • Anatomical abnormalities, such as diverticulosis or previous intestinal surgery can create pockets where bacteria can proliferate.

Diagnosis of SIBO

  • Breath Testing: Non-invasive test that measures hydrogen and methane gas production by bacteria in the small intestine after drinking a sugar solution.
  • Small intestine aspirate and fluid culture. This is currently the gold standard test for bacterial overgrowth. However, it’s a more invasive procedure

Complications of SIBO

  • Bacterial overgrowth can cause deficiency in macro- and micronutrients:
    • The bacteria may consume Vitamin B12, leading to deficiency.
    • Malabsorption of fats: night blindness (Vitamin A), bone pain and muscle weakness (Vitamin D), neurological problems (Vitamin E), to bleeding and clotting issues (Vitamin K) and deficiency in essential fatty acids
    • Poor iron absorption causing iron deficiency, which may or may not cause anemia. Other symptoms are fatigue, weakness, and hair loss and hypothyroidism
    • Zinc deficiency leading to poor wound healing, loss of taste and smell, and a weakened immune system.
    • Decreased calcium absorption, potentially leading osteoporosis and muscle cramps.
  • Chronic diarrhea dehydration, and electrolyte derangements.
  • Reduced nutrient absorption can result in weight loss.
  • Damage of the gut lining due to long-standing inflammation causing the development of leaky gut
  • Mental disorders such as depression and anxiety due to the two-way relationship between the gut and the brain (The gut-brain axis)

Treatment of SIBO: A Functional Medicine Approach

  • Reducing nutrient availability for the bacteria through a low FODMAP diet, Specific Carbohydrate Diet (SCD), or Elemental diet.
    • This reduces the amount of nutrition for harmful bacteria
    • Improves the gut microbiota
    • Reduces gut transit time
  • Probiotics and Prebiotics: These can help restore a healthy gut microbiome.
  • Antibiotics, such as Rifaximin may be used. However, SIBO may re-appear and generally antibiotics should be reserved it other measures are not successful or more severe cases.
  • Herbs with antimicrobial effects can be used as alternatives to antibiotics with less risk of resistance issues and side effects.
  • Medications or natural substances can be used to enhance gut motility.
  • Nutrient Supplementation to correcting nutrient deficiencies is crucial for overall health.

How DMH Functional Medicine Can Help?

Our approach respects each patient’s individuality, considering their unique situation taking into account their medical history, test results and lifestyle factors and preferences.

We provide dietary recommendations to help manage SIBO and support overall health.

Long-Term Support: Our team offers ongoing care, adjusting treatment plans as necessary to ensure successful outcomes.


  • Quigley, E. M. (2011). Small intestinal bacterialovergrowth: what it is and what it is not. Current opinion in gastroenterology, 29(2), 140. 2. Rezaie, A., Buresi, M., Lembo, A., Lin, H., McCallum, R., Rao, 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.
  • Dukowicz, A. C., Lacy, B. E., & Levine, G. M. (2007). Small intestinal bacterial overgrowth: a comprehensive review. Gastroenterology & hepatology, 3(2), 112.
  • Bures, J., Cyrany, J., Kohoutova, D., Förstl, M., Rejchrt, S., Kvetina, J., … & Kopacova, M. (2010). Small intestinal bacterial overgrowth syndrome. World journal of gastroenterology: WJG, 16(24), 2978.
  • Ghoshal, U. C., & Srivastava, D. (2014). Irritable bowel syndrome and small intestinal bacterial overgrowth: meaningful association or unnecessary hype. World journal of gastroenterology: WJG, 20(10), 2482.
  • Jacobs, C., Coss Adame, E., Attaluri, A., Valestin, J., & Rao, S. S. (2013). Dysmotility and proton pump inhibitor use are independent risk factors for small intestinal bacterial and/or fungal overgrowth. Alimentary pharmacology & therapeutics, 37(11), 1103-1111.
  • Pimentel, M., Chow, E. J., & Lin, H. C. (2000). Normalization of lactulose breath testing correlates with symptom improvement in irritable bowel syndrome: a double-blind, randomized, placebo-controlled study. The American journal of gastroenterology, 95(2), 350-355.
  • Chedid, V., Dhalla, S., Clarke, J. O., Roland, B. C., Dunbar, K. B., Koh, J., … & 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.