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7 Underlying Causes of SIBO That You Might Be Missing

by Romilly Hodges, MS, CNS

Sometimes a simple low FODMAPs diet, or a course of prescription or botanical antimicrobials, is enough to shift a case of SIBO. But if your experience is anything like ours, some cases are much harder to address and can be much more prone to recurrence. If you’re presented with a difficult SIBO case (or if you yourself feel like a difficult case!), read on to find out what else you should be thinking about.

What is SIBO?

SIBO stands for Small Intestinal Bacterial Overgrowth. Normally, the bulk of our gut microbiome resides in the large intestine. In SIBO, we see an overgrowth of bacteria (even otherwise healthy bacteria) in the small intestine, where they are not usually present to such a high degree. Those bacteria are then able to act on poorly-digested, fermentable carbohydrates, producing uncomfortable symptoms such as bloating, gas, abdominal pain, diarrhea and/or constipation.

The effects of SIBO can extend beyond direct gastrointestinal symptoms. The excess levels of bacteria excrete acids that can underlie some neurological symptoms including brain fog and fatigue. Increased gut permeability can occur causing translocation of bacteria and insufficiently digested food particles that trigger immune activation that can lead to pain and other symptoms. It also predisposes an individual to food sensitivities. Nutrient deficiencies can arise as the bacteria consume some of the ingested foods; B12 and iron, for example, which can lead to anemia, and deconjugation of fatty acids from bile that reduces absorption of fat-soluble vitamins. Patients with SIBO also tend to have altered secretory IgA values, demonstrating that SIBO directly alters immune activity in the gut.

Practicing Functional Medicine thinking

Addressing SIBO with diet and botanicals, while clearly important, represents a rather ‘top down’ approach to treatment. In many cases, we may need to be combining that with ‘bottom up’ (root cause) support.

In Functional Medicine, we should always be thinking about the root cause, regardless of the condition we’re trying to address, and SIBO is no exception. There are a number underlying factors that may need to be considered to support successful resolution and prevent recurrence of SIBO.

For those that are familiar with the terminology used by the Institute for Functional Medicine, we’ll review these as Antecedents, Triggers and Mediators (ATMs for short). Don’t worry, if you’re not yet familiar with these terms, you’ll still be able to follow along. Since the pathophysiology may be better understood this way, we’re going to start with Mediators first, and work backwards.

SIBO mediators

Mediators are factors that contribute to the ongoing, or active, state of the condition, in this case of bacterial overgrowth. Three primary mediators stand out:

1. Reduced transit time. The migrating motor complex is critically important for enabling peristalsis, the smooth muscle contractions of the intestines that propel its contents along, and avoiding stagnancy within the lumen of the small intestine. A disruption to the migrating motor complex encourages bacterial overgrowth and prevents excess bacteria from being cleared out of the small intestine. This is the reason why SIBO protocols often include motility agents, or advice to space meals 4-5 hours apart.

2. Increased transit time. Food that passes through the bowel too quickly, such as in short bowel syndrome, can also be problematic since there is insufficient time for proper digestion and absorption.

3. Altered digestive secretions. Sufficient stomach acid, bile and enzymes all act to keep bacterial levels in the small intestines in check. If those digestive secretions are compromised, bacteria can start to flourish. Once again, SIBO protocols may also include digestive support to replace and/or improve digestive secretions. This can be accomplished with dietary supplements as well as practices that improve digestion, such as thorough chewing and mindful eating.

SIBO triggers

Single or short-term events are known to trigger SIBO in some cases. Examples include acute gastroenteritis, acute stress, or medications such as proton-pump inhibitors which inhibit gastric acid secretions.

If the SIBO was triggered by one of these events, without any of the antecedents that we will review next, then it is more likely (though not always guaranteed) that diet plus a course of antimicrobial botanicals will be effective at resolving the condition. If the trigger is no longer present, of course.

However, if any of the following antecedents are present to a sufficient degree, causing the SIBO mediators to persist, then they may be interfering with long term resolution of the SIBO.

SIBO antecedents

Here’s where some of the most difficult cases of SIBO may be getting stuck. These predisposing factors were likely present before the onset of SIBO and set the stage for the condition to take hold. By simply addressing the bacterial overgrowth directly (or ‘top down’), we may not have addressed factors that will encourage SIBO to return at the first opportunity. This is not an exhaustive list, but represents some more common underlying issues:

1. Hypothyroid. Low thyroid function can affect all cells of the body, including the cells of the GI tract. Hypothyroid can reduce the activity within the gastrointestinal tract, slowing the migrating motor complexes that trigger peristalsis.

2. Diabetes. We know that the oxidative damage caused by high blood sugar in diabetes can lead to deterioration of vision, kidney function and peripheral blood vessels. And it can also damage the nerves that regulate and control intestinal migrating motor complexes.

3. Chronic stress. When the body enters the sympathetic fight-or-flight state, gastric function is altered. We are not in the rest-and-digest state anymore. This also affects the enteric nervous system that controls the migrating motor complex. In our experience, stress appears to be a contributing factor in virtually all cases to some extent.

4. Depressed immunity. Various immunodeficiency syndromes have been associated with increased risk for bacterial overgrowth, including IgA deficiency. Secretory IgA in the gastrointestinal tract is the largest fraction of immunoglobulins secreted in the body, and aids in preventing bacterial proliferation.

5. Stealth infections. The potential complications arising from acute or chronic infections from lyme or other tick coinfections are many, and include gut dysfunction, even so-called ‘palsy of the gut.’ Gut dysmotility has been associated with infectious agents including varicella zoster, Estein-Bar virus, and Lyme disease.

6. Abdominal adhesionsAbdominal adhesions, otherwise known as scar tissue, which can arise from chronic inflammation (e.g. Crohn’s Disease), infection or surgery, can create an obstruction or distortion of the intestines and/or impair the enteric nervous system’s migrating motor complex, both of which can predispose to SIBO.

7. Excess estrogens. Estrogen-induced gallstones are a common form. Excess estrogens can inhibit the excretion of bile saltsfrom the liver into the intestines. Since bile salts have antimicrobial activity, their deficiency can be a predisposing factor for SIBO. Estrogen also delays gastric emptying and motility.


Romilly Hodges, MS, CNS, holds a master’s degree in Functional Nutrition from the University of Bridgeport, CT, and is a Certified Nutrition Specialist (CNS). She is passionate about the power of food to nourish and heal the body.

Reposted with permission from Dr. Kara Fitzgerald www.drkarafitzgerald.com

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