Natural Health and Wellness for the Whole Family

Why do I have SIBO?

By Joanne Aponte, ND July 18, 2019

We see a lot of Small Intestinal Bacterial Overgrowth (SIBO) at our clinic and still, the answer to this question is not an easy one. I always ask myself “WHY does this person have SIBO?” and I do my best to figure out the answer.  If we can identify the WHY, that is our best chance at preventing SIBO from returning and for more lasting relief of symptoms.

When there is an overgrowth of bacteria in the small intestine, IBS–like symptoms may develop. The bacteria in the gut produce gas, which leads to bloating, abdominal pain, belching, bowel irregularity and possibly reflux. We now know that SIBO is a common underlying cause of IBS. If you are unfamiliar with SIBO, read this.

In order for SIBO to develop, there has to be a malfunctioning or breakdown of the “housekeeper” of the small intestine. This “housekeeper” is a set of nerves called the Migrating Motor Complex (aka MMC). It has the job of sweeping and cleaning bacteria and food out of the small intestine and pushing it into the large intestine. The MMC works like washing the dishes after you eat a meal.  SIBO develops when this breaks down and bacteria are not efficiently cleared out of the small intestine. To learn more, read this.

There are many possible causes and reasons why a person might develop SIBO. Many of the causes listed below lead to a malfunctioning of the migrating motor complex, resulting in bacteria building up in the small intestine where they can wreak havoc.

When I am working with patients with SIBO, I go through a check list similar to the one below to help me figure out the contributing risk factors and causes. To successfully treat SIBO, we need to address the cause and risk factors as best as possible. There are natural protocols to address many of the below causes and risk factors of SIBO.  Sometimes this is easy and straightforward, other times it is quite a challenge and may require referrals to specialists.

Underlying causes and risk factors of SIBO

  1. Food poisoning and stomach flu
    • This is theorized to be the most common cause of IBS and SIBO. For some people who get food poisoning or a stomach flu, the bacterial toxins actually damage the migrating motor complex. This damage, unfortunately, may be permanent and SIBO is likely to be chronic and need ongoing management.
  2. Medications such as antibiotics, opiates (taken for pain) and proton pump inhibitors (used for acid reflux)
    • Antibiotics may lead to slow motility in the small intestine and thus inefficient cleansing action. Proton pump inhibitors which suppress stomach acid can lead to bacterial overgrowth because there is not enough stomach acid to kill bacteria entering the stomach. Opiates and pain medications slow down the motility in the intestinal tract leading to a build up of bacteria.
  3. Diseases that cause slow motility of the digestive tract
    • This includes Diabetes, Ehlers Danlos, Scleroderma, Traumatic Brain injuries, Lyme disease, Parkinson’s and POTS. This group of conditions is challenging to treat and SIBO is likely to recur and need ongoing management. To fully resolve SIBO the underlying disease needs to be treated, however for several of these diseases listed, there is no known complete cure. 
  4. Hypothyroidism
    • A low functioning thyroid can lead to slower motility in the intestinal tract which leads to the buildup of bacteria in the small intestine. Thyroid medication may be needed to achieve better function. Other times a more natural approach is successful at improving thyroid function. This may include targeted nutrients such as iodine, zinc, iron and selenium, and adrenal support.
  5. Dysfunctional ileocecal valve
    • The ileocecal valve is a flap of tissue that connects the large intestine to the small intestine. It should remain closed most of the time to prevent bacteria in the large intestine from migrating upward into the small intestine where they can cause problems. If this valve is stuck open or not able to close tightly, bacteria from the large intestine migrate upwards into the small intestine. Certain diseases, food intolerances and stress may lead to a weak IC valve that does not close properly. We use Chlorophyll, digestive enzymes such as HCL and pepsin to help the IC valve close tightly. There are also abdominal massage techniques that work on the IC valve – I often refer patients to a visceral massage therapist to help address this piece.
  6. Low stomach acid
    • One function of the acid in the stomach is to kill bacteria that enter through the mouth when we eat food. If there is not enough acid to kill this bacteria, the organisms may travel to the small intestine. Hypothyroidism, stress and some nutrient deficiencies can lead to low stomach acid. A  supplement of the digestive enzyme Betaine HCL, herbal bitters or apple cider vinegar can be used to increase stomach acid.
  7. Digestive enzyme or bile deficiency
    • Digestive enzymes and bile help us digest our food, but also help kill unwanted bacteria in the intestinal tract and promote movement through the intestine. Taking a supplement of digestive enzymes or bile acids can be very helpful at preventing a recurrence of SIBO.
  8. Things that cause obstruction  or scar tissue in the abdomen
    • Endometriosis, appendicitis, Crohn’s disease and abdominal surgeries. When there is scar tissue in the intestinal tract, food and bacteria  do not efficiently move through and out of the intestine. Scar tissue and adhesions can be addressed with a very specialized visceral therapy (Clear Passage) or frequency specific microcurrent.
  9. Stress
    • Turns off the migrating motor complex and can shut down gastrointestinal movement. Effective stress management techniques and healthy lifestyle practices are a huge piece. Simple things like chewing food until it’s a liquid and eating slowly are helpful. I often recommend Buteyko breathing to patients when this is a contributing factor.
  10. Weakened immune system
    • Bacteria may overgrow if the immune system is not strong and healthy enough to kill the micro-organisms that enter the intestinal tract. This may occur when there is significant immune suppression in diseases such as HIV or Lyme disease.

As you can see, there is a pretty long list of potential causes and risk factors. Some of these are easily addressed and others are not. When the underlying cause of SIBO cannot be identified or effectively treated, there is still so much that can be done to manage the symptoms and improve quality of life. SIBO symptoms can have a huge negative impact on your life, but there are many natural therapies that are very effective at managing the condition and reducing severity of symptoms. Even if the cause of your SIBO cannot be treated, you do not have to live in pain or discomfort. There are many lifestyle, nutritional and natural remedies for addressing the symptoms and to help address your individual risk factors.

Editor’s Note: The information in this article is intended for your educational use only. Always seek the advice of your physician or other qualified health practitioners with any questions you may have regarding a medical condition and before undertaking any diet, supplement, fitness, or other health program.


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