Condition Overview

SIBO: Small Intestine Bacterial Overgrowth

SIBO: Overview, Symptoms, Treatments, Diet & More

SIBO is a relatively new condition identified by the medical community. Being diagnosed with SIBO can be a confusing and frustrating situation because:

  • Not every doctor is aware of it or understands how to treat it
  • It’s hard to diagnose
  • There are numerous root causes
  • There are multiple ways to treat it
  • There are a plethora of diets and supplements claiming to help

What is Small Intestine Bacterial Overgrowth (SIBO)?

There is no consensus on the specific definition but it is generally accepted that SIBO is a condition in which bacteria normally found in the colon overgrows in the small intestine and causes abnormal digestive symptoms. Essentially, it’s too many good bacteria in a place it doesn’t belong.

What Are the Symptoms of SIBO?

The following symptoms are most commonly associated with SIBO:

  • Diarrhea
  • Abdominal pain
  • Gas & bloating
  • Constipation
  • Nutrient deficiencies, anemia & weight loss

Because these are not symptoms specific to SIBO, it is hard to diagnose and must be differentiated from a functional gut disorder or another condition.

What Causes SIBO?

There is no one single known cause. It can occur when there is breakdown in one or more of your body’s innate mechanisms designed to keep bacteria from colonizing in the small intestine such as:

  • Anatomical Abnormalities – resulting from abdominal surgery such as adhesions or diverticula.
  • Low Stomach Acid – Gastric acid in the stomach kills many bacteria before exiting the stomach. Low stomach acid levels can raise gastric pH leading to an overgrowth of bacteria. What can cause low stomach acid?
    • Medications such as narcotic pain medications and proton pump inhibitors taken for conditions such as acid reflux, heartburn, GERD, LPR, ulcers, gastritis and for H. pylori.
    • Aging – As we grow older, we can produce lower levels of stomach acid.
  • Bile & Enzyme Deficiencies – They limit growth of bacteria in the small intestine. What can cause these deficiencies?
    • Bile deficiency can be caused by dysfunction of the gallbladder and/or liver.
    • Digestive enzymes need stomach acid to activate, so once again, we see the need for stomach acid. Also, damage to the small intestine caused by inflammation from food sensitivities, medications, toxins and chronic stress (via stress hormones) can cause lower production of digestive enzymes. The overgrowth of bacteria that leads to SIBO can also cause digestive enzyme deficiency resulting in a never-ending cycle of poor digestive function.
  • Poor Motility – Not to be confused with constipation, poor motility refers to the slow function of the migrating motor complex (MMC). These are the muscles in the digestive tract that move food, bacteria and toxins down and out. The MMC is crucial to maintaining balanced gut bacteria populations. What can cause poor motility?
    • Conditions such as Parkinson’s, diabetes, pancreatitis and hypothyroidism
    • Narcotic pain medications
    • Low stomach acid related to aging
  • Ileocecal Valve Malfunction – This is the valve between the small intestine and the colon. It prevents retrograde movement of bacteria from the colon to the small intestine.

It’s important to note that SIBO is a result of one of the above conditions. The root cause must be resolved or there is a high chance for reoccurrence.

SIBO & Other Conditions

SIBO occurs at a relatively high rate with the following conditions:

  • Abdominal surgery
  • Celiac disease
  • Chronic fatigue syndrome
  • Chronic pancreatitis
  • Crohn’s disease
  • Endometriosis
  • Fibromyalgia
  • Irritable Bowel Syndrome (IBS)
  • Low thyroid function (hypothyroid or Hashimoto’s thyroiditis)
  • Muscular dystrophy
  • Ulcerative colitis

How Does SIBO Cause Symptoms & Intestinal Damage?

  • The bacteria that colonize in the small intestine ferment carbohydrates resulting in gas.
  • This overgrowth of bacteria compromises enzyme function by injuring the intestinal lining, affecting digestion and nutrient absorption.
  • Damaged intestinal lining can lead to increased intestinal permeability, otherwise known as “leaky gut”.
  • Bacteria consume your nutrients such as vitamin B12 and protein, which can lead to deficiency.
  • Bacteria may deconjugate bile acids, which can lead to fat malabsorption and deficiencies of fat-soluble vitamins.
  • Bacteria can produce various endotoxins such as ammonia and d-lactate that may have effects across the whole body.

How is SIBO Diagnosed?

There is no gold standard and all methods have limitations. There are often false negative/positive results.  Three methods are used (more than one can be used for a more confident diagnosis):

  1. Endoscopy with culture of the small intestine bacteria. This option is invasive & expensive.
  2. A lactulose or glucose breath test, which measures hydrogen and methane. These gasses are not produced by humans and their presence signify the metabolic byproducts of carbohydrate fermentation by bacteria. These tests are relatively inexpensive, not invasive and often performed at home. 
  3. Trial of antibiotics to determine if symptoms improve.

How is SIBO Treated?

There are three main principles in treating SIBO:

1. Treat the underlying cause

SIBO can be a relapsing condition because it’s a secondary condition. The best results involve treating the root causes, if possible.

2. Eradicate the overgrowth of bacteria

Doctors may prescribe antibiotics and/or herbal antimicrobials along with other supplements such as fiber or probiotics. There are numerous protocols a doctor may employ based on the outcome of the breath test, medical studies or clinical results in their own client population. Multiple rounds of treatment may be necessary.

Rifaximin is the most studied antibiotic for SIBO and may be the preferred option because it stays local to the small intestine and doesn’t disrupt the good bacteria in the colon.

The Elemental Diet is a physician-monitored liquid diet. It has been shown to normalize breath tests. This may be an appropriate approach for those allergic to antibiotics or for those who don’t respond to them for treatment.

3. Address nutrient deficiencies

Nutritional support is required in those with nutrient deficiencies, malnutrition and weight loss.

What is Best Diet for SIBO?

Diet does not cure SIBO but rather helps manage symptoms and create a hospitable environment for healing. There are a variety of diets that reduce fermentable carbohydrates to varying degrees. We work with our clients to select a diet and modify it based on severity of symptoms, underlying cause, and presence of other health conditions.

It’s important to note that these diets are not forever diets. They are tools used to help manage symptoms, identify food sensitivities/intolerances and to help the digestive system heal. Once symptoms have improved, we can carefully and systematically reintroduce previously restricted foods. The goal is to liberalize the diet as much as possible while limiting symptoms.

Below are the most widely used SIBO diets in order of carbohydrate restriction.  We find that when we help our clients improve digestive function, they don’t need to be on such restrictive diets. 

Keep in mind that SIBO diets are meant to be short term elimination diets to help manage symptoms and heal the gut.  Often the more restrictive diets do more harm than good. 

  • FODMAP is an acronym for types of carbohydrates.
  • This is a well-studied diet for Irritable Bowel Syndrome (IBS), Irritable Bowel Disease (IBD) and other GI conditions with high success rates.
  • It is the least restrictive in that it allows certain vegetables, fruit, nuts, grains, legumes, low-lactose dairy, etc.
  • The Monash University developed the diet and regularly tests new foods for FODMAPS. It offers an app with comprehensive list of low/medium/high FODMAPs and serving sizes.

The Fast Tract Diet

  • Developed by Dr. Norm Robillard, a microbiologist to address many gut disorders related to SIBO including IBS, GERD, LPR, IBD and more.
  • It is similar to the low-FODMAP diet in that it restricts fermentable carbohydrates but uses a different mathematical formula.
  • It focuses on reducing the total amount of fermentable carbohydrates.
  • Offers books and an app that can track Fermentable Points (similar to Weight Watchers) so users can stay within a point-range based on the severity of their symptoms.
  • May be useful for those who need more structure than the low-FODMAP provides and less restriction of the other diets.

Specific Carbohydrate Diet (SCD)

  • Popularized by Elaine Gottschall in the book Breaking the Vicious Cycle.
  • The SCD has been studied and is successful in managing IBD.
  • The diet restricts grains, starchy vegetables, lactose, some legumes and any sweeteners other than honey, saccharine and occasional stevia.
  • It involves an introductory phase and reintroductions as the gut heals with personalization based on what is tolerated.

SIBO-Specific Diet

  • Developed by Dr. Alison Siebecker, a naturopathic doctor specializing in SIBO.
  • It’s a combination of the Specific Carbohydrate Diet & the Low-FODMAP diet.
  • It’s the most restrictive of the SIBO diets and recommended to use if others aren’t providing enough relief.

SIBO Bi-Phasic Diet

  • A 3-month protocol developed by Dr. Narala Jacobi, a naturopathic doctor specializing in SIBO.
  • This is a variation of the SIBO-Specific Diet but implemented in phases.

Paleo Diet

  • Restricts grains, legumes, dairy, sugar, processed foods, alcohol.
  • If necessary, you may need to restrict to low-FODMAP fruits & vegetables.

Gaps Diet

  • Developed by Dr. Natasha Campbell-McBride, author of the Gut and Psychology Syndrome: Natural Treatment for Autism, Dyspraxia, A.D.D., Dyslexia, A.D.H.D., Depression, Schizophrenia for clients suffering with neurological and GI disorders.
  • It has not been studied in clinical trials for any of the conditions it claims to treat.
  • It is a variation of the Specific Carbohydrate Diet.
  • Restricts all commercial dairy, grains, starchy vegetables, processed foods and refined carbohydrates foods.
  • There is a staged strict introductory phase followed by the full GAPS diet, then the reintroduction phase, all of which can last up to 2 years.

How to Prevent SIBO From Relapsing

SIBO is a relapsing condition, especially if the underlying causes are not identified and corrected. Options include:

  • Watchful observation and retreatment if necessary
  • Promotility drugs (also known as prokinetics) to address the poorly functioning migrating motor complex (MMC). Prescription motility drugs used for SIBO prevention include erythromycin, cisparide and prucalopride. Herbal prokinetics include Iberogast, ginger and Motilpro.
  • Lower carbohydrate diet
  • Use of select probiotics/prebiotics. A study indicates that probiotics may be protective for prevention of SIBO in those at high risk.

How to Support Motility & the Migrating Motor Complex

The Migrating Motor Complex (MMC) is the housekeeping function of the digestive system. It involves involuntary muscular contractions of the stomach, small intestine and colon to help sweep food, waste and bacteria down and out. It only occurs in the fasted state approximately 2 – 3 hours after your last meal and continues for about 90 minutes but this process slows at night. So what can you do to enhance motility and prevent SIBO?

  • No snacking – Space out meals by at least 4 hours to allow the MMC to work effectively.
  • Fast – for at least 12 hours between dinner and breakfast the next day.
  • Improve the stress response – As we have learned, chronic stress hormones can damage the intestinal lining. Stress also reduces vagal nerve function, which is required for the MMC to work properly. Stress has been shown to inhibit contractions of the MMC. Read more about how to improve the stress response.

Our Functional Nutrition Approach to SIBO

SIBO is a challenging condition that often relapses. Gut-healing protocols and addressing the root cause are essential to long lasting relief. We work with clients to:

  • Elicit a detailed health history to determine the potential root cause(s) and concurrent health conditions
  • Understand symptoms and triggers
  • Test for SIBO using at-home breath tests
  • Recommend a personalized SIBO diet to implement during antibiotic treatment
  • Implement a gut-healing protocol after treatment based on symptoms, health history, concurrent conditions and preferences
  • Address nutrient deficiencies, if necessary
  • Advise on lifestyle changes and stress reduction techniques
  • Reintroduce foods slowly and systematically to determine food sensitivities and intolerances
  • Celebrate the victories every step of the way!


View References

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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.

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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), 2482–2491.

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Khalighi, A. R., Khalighi, M. R., Behdani, R., Jamali, J., Khosravi, A., Kouhestani, S., … Khalighi, N. (2014). Evaluating the efficacy of probiotic on treatment in patients with small intestinal bacterial overgrowth (SIBO) – A pilot study. Indian Journal of Med Res, 140(5), 604–608.

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