What is Small Intestinal Bowel Overgrowth?

Small intestinal bowel overgrowth (SIBO) is a condition where abnormally high numbers of bacteria exist in our small intestine. SIBO is a type of dysbiosis. Dysbiosis is a condition where abnormally high levels of bacteria, yeast, and/or archea (other single cell organisms) are in the small intestine. In my opinion, SIBO is a hugely overlooked condition. In fact, I think too many practitioners ignore the bacteria and archea overgrowth and simply diagnose individuals with a Candida problem. Candida overgrowth can occur with or without bacterial overgrowth. The improper diagnosis and treatment can be solved by use of important lab analysis discussed later in this article. Most often the bacteria that overgrow are our beneficial bacteria that get out of control. Bacterial overgrowth has been shown to be present in 84% of irritable bowel syndrome (IBS) patients. Treatment leads to a 75% have a reduction of symptoms.1,2 One study showed that 100% of people with fibromyalgia test positive for SIBO.16 Bacterial overgrowth in the small bowel has been implicated as an important factor to the following symptoms and associated diseases:

  • Gas
  • Bloating
  • Abdominal pain
  • Heartburn (GERD)
  • Nausea
  • Constipation
  • Diarrhea
  • Chronic Fatigue
  • Skin disorders
  • Joint pain
  • Headaches
  • Adrenal Fatigue
  • Malabsorption of fats, iron, vitamin D, vitamin K, B12, carbs
  • Osteoporosis
  • Gallstones
  • Lactose intolerance
  • Intestinal hyperpermeability (leaky gut)
  • Food sensitivities
  • Irritable bowel syndrome (IBS)
  • Ulcerative Colitis
  • Poor digestion-especially carbs
  • Autism
  • Fibromyalgia
  • Systemic sclerosis
  • Diverticulitis
  • Restless leg syndrome
  • Depression/Anxiety
  • Interstitial cystitis
  • Autoimmune disorders
  • Hypothyroidism
  • Crohn's disease
  • Celiac disease
  • Obesity and Diabetes
  • and even more

This list is an overwhelmingly large (and incomplete) list of problems related to a single cause.  I will attempt to concisely explain how this comes to be and what can be done about it.


There are 4 major causes and many contributing causes of SIBO. The three major causes are:

  1. Bactericidal GI secretion
  2. Migrating Motor Complex (MMC)
  3. Ileocecal Valve Dysfunction
  4. Intestinal Damage

1. Bactericidal Gastrointestinal Secretions

Our body produces digestive juices that are antimicrobial, namely stomach acid. Our food is often covered with bacteria, viruses and yeasts. This is usually not a problem because many of theses microbes cannot survive in the presence of stomach acid. If you take medication for heartburn, especially proton pump inhibitors, your chances of having SIBO are high. 10,11 In fact, SIBO may be the cause of the heart burn symptoms to begin with. Gastic bypass surgery increases risk for SIBO because it reduces not only acid production but how well we digest and absorb our food.12,13

Our intestinal tract secretes an important antibody called IgA (see wikipedia IgA.) This is part of our immune system. If we are stressed these antibodies are lowered, weakening our immune system and allowing for bacterial overgrowth.

2. Migrating Motor Complex

The migrating motor complex (MMC) is a neurological system that sweeps stuff down our digestive tract.  This makes sense in terms of moving our food down the digestive tract.  However, an important function of the MMC is to sweep down bacteria so they cannot over populate the small bowel.  MMC dysfunction causes stasis (constipation) and allows for reproducing bacteria to achieve higher than normal numbers resulting in SIBO.

Constipation is a symptom of dysfunction in the migrating motor complex.  Things that affect this system are:

  • Emotional stress causes increased cortisol, coricotropin and corticotropin releasing factor, these hormones slow the migrating motor complex in stomach and small intestine.4
  • Opiates (pain pills)
  • Diabetes damages the nerves of the MMC causing constipation and SIBO.3 This is called diabetic gastroparesis
  • Poor Diet
  • Insufficient water intake

3. Ileocecal Valve Dysfunction

The Ileocecal valve is located between the small and large intestines. This valve prevents back flow from the large intestines, where high levels of bacteria live, into the small intestines. If back flow is permitted, many of the large bowel bacteria will overgrow into the small bowel causing SIBO.5

4. Intestinal Damage

Bacteria feed on carbohydrates (sugars, starches, fiber, etc). We have special enzymes in the lining of our gut that help digest our food. If the lining in our intestinal tract is damaged, our ability to digest the carbs we eat is decreased. In addition to reduced digestion, a damaged intestinal lining reduces proper absorption of our food. Poor digestion and poor absoption leave more food for the bacteria to consume resulting in bacterial overgrowth. A major cause of intestinal damage is a poor diet.22,23,24,25 The worst diet in terms of intestinal damage is the standard American diet. In one study people placed on a "Western-style diet" for one month showed a 71% increase in a marker for intestinal damage compared to those on a healthy diet who showed a reduction of this same marker by 31%.23

Other significant causes of SIBO include:

  • Infectious gastroenteritis from campylobacter, salmonella, shingell, E. coli, clostridium, giardia or a virus.6
  • Blind loop perforation after side-to-side ileocononic anastomosis (removal of a section of bowel that bypasses the ileocecal valve)7
  • Moderate to heavy alcohol consumption8
  • Intestinal damage due to NSAIDs (Ibuprofen, Asprin, naproxen)9*
  • Recurrent use of antibiotics causes a disruption in normal bacterial balance and has been implicated as a cause of dysbiosis. This seems to be common in SIBO patient health histories.
  • The standard American diet plays an extreamly large role in starting this condition. Poor diet is known to cause constipation, iliocecal valve dysfunction, poor digestion, intestinal damage and leaky gut and altered gut bacterial concentrations.22,23,24,25

Key Indicators that you might have SIBO

Dr. Allison Siebecker, an authority on SIBO, gave what she called "key indicators for Small Intestinal Bacterial Overgrowth (SIBO)."20 If you have experienced these things you may have SIBO.

  • Improvement in gas/bloating while taking antibiotics.
  • Worsening of GI complaints with probiotics containing prebiotics.  Prebiotics are food for the bacteria.
  • Fiber worsens constipation or other GI symptoms (soluble fiber is a prebiotic).
  • Celiac patient doesn’t improve sufficiently with gluten free diet.
  • Chronic GI symptoms began after taking opiates (pain pills) due to their bowel slowing effect, affects MMC.
  • Chronic low blood ferritin (iron deficient anemia) with no other cause: bacteria uses up your iron.
  • Pancreas is obscured by a gas bubble on a C.T. scan.

Effects of bacterial overgrowth - a very vicious cycle

As the bacteria over grow they damage the lining of the intestinal tract.  Bacteria produce and enzyme called glycosidase that destroy brush border enzymes in our intestinal lining.  This reduction in our digestive enzymes reduces our ability to digest and absorb our food, providing more food for the bacteria allowing them to become even more overgrown.  A vicious cycle.

Bacteria ferment the carbohydrates in our diet producing large amounts of gas and abdominal discomfort. This is a common symptom of lactose intolerance. According to Elaine Gottschall, an individual with SIBO will produce 100 times more gas from an ounce of milk than someone with normal bacterial numbers. 14 This gas will exit the body through eructation (belching) or flatulence. The increased gas can also cause heartburn and acid reflux (GERD). The gas, particularly methane gas, further perpetuates the cycle by causing a reduction in GI motility (constipation). The gas induced constipation leads to more overgrowth promoting this vicious cycle.

As the bacteria continue to damage the intestinal lining, intestinal hyperpermeability (leaky guy) develops. Leaky gut has been associated with food allergies and/or intolerance, autoimmune conditions and fibromyalgia. 15 Damage to the intestines will create inflammation, pain and a stress response that have linked SIBO to fibromyalgia. In fact, fibromyalgia patients have a higher rate of positive lactulose breath tests (a test for SIBO) than do irritable bowel sydrome (IBS) patients. 100% for fibromyalgia vs 84% for IBS. 16 I believe that this stress response is the cause of many adrenal fatigue problems. This may be especially true in patients who do not respond to traditional adrenal healing strategies. SIBO may be the underlying cause.

The over grown bacterial population will even consume much or our needed nutrients. SIBO has been associated with oseoporosis and anemia. 17

Testing is how we diagnose SIBO

Hydrogen and Methane Breath Test example from GEnova Diagnostics

Breath testing has been the standard method of testing for SIBO.  Much of the research has been done using this method. It is performed by drinking lactulose, a non-absorbable sugar.  The lactulose is then fermented by the bacteria in the small bowel producing hydrogen and methane gases.  Some of these gases are absorbed into the blood and exit by way of the lungs.  You breathe into a bag, hook up a vacuum tube that sucks in the breath and ship it off to the lab. You collect breath samples over 120 minutes to see where the overgrowth is most prominent.

Organic acid test example from Genova Diagnostics

Organic Acid Testing is my preferred method of testing.  It is a simple urine test  that measures metabolites (by products) of the microoganisms in our gastrointestinal tract.  This will not only provide the accurate diagnosis of SIBO but will also give insight into other problems that may exist.  I believe organic acid testing gives important clinical information to properly treat this condition.  For example an organic acid test provides information regarding the species of overgrowth, like Lactobacillus Acidophilus. This is important because if you have an overgrowth of L. acidophilus you would want to avoid a probiotic that includes that bacteria. Organic Acid testing also will gives us information about Candida overgrowth. If you have an overgrowth of Candida then antifungals must also be used as part of proper treatment. 

The organic acid test also tests for overgrowth of Clostridium. Testing for Clostridium is important because it can effect conversion of dopamine to norepinephrine and epinephrine. This is significant in patients with autism, adrenal fatigue, anxiety and other mental health concerns.21 If there is Clostridium in your bowels and you don't manage it properly you could end up with a severe Clostridium infection.18

This is why it is so important to test before starting any treatment regiment.

What can be done

First you need to confirm the diagnosis so you aren't mistreating.  It is a big mistake to follow an internet protocol without proper testing.  All of these symptoms can be caused by many things and mistreatment may make things worse.

Once you have a proper diagnosis, treatment can begin. If you do in fact have SIBO, prescription antibiotics or natural antimicrobials have been shown to be equally effective, though the natural route had fewer side effects.18

I recommend that people follow the specific carbohydrate diet (SCD) as outlined by Elaine Gottschall, B.A., M.Sc. in her book "Breaking the Vicious Cycle: Intestinal Health Through Diet"14 There are other diets out there that will also be beneficial. The GAPS diet and the low FODMAP diet have been shown to be beneficial.

After making the dietary changes and following an antimicrobial treatment, I follow up with a protocol that helps accelerate the healing of the gut lining. This should promote proper digestion, reduce intestinal hyperpermeability (leaky gut) and hasten the reduction of symptoms.

If you believe you have SIBO and are interested in a done for you meal plan I recommended that you get one the the two options found here:  Meal Plans


Small intestinal bowel overgrowth can be a very challenging condition. It is a contributing factor in significant conditions like fibromyalgia, chronic fatigue, IBS and inflammatory bowel diseases (Crohn's disease and ulcerative colitis).19 If you are suffering from symptoms that makes you suspect of SIBO you should seek help from a professional who is trained specifically in the diagnosis and treatment of SIBO. If are diagnosed and treated appropriatly for SIBO you should notice significant improvent in your symptoms as your body heals and begins to fuction properly.


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