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To understand what causes it let’s first explore the endogenous defence mechanisms that help prevent small intestine bacterial overgrowth.

These include:

  • Secretion of hydrochloric acid produced in the stomach
  • Gut motility
  • An intact ileo-cecal valve
  • Secretory immunoglobulins (sIgA)
  • Bacterio-static properties (stops bacteria from reproducing) of pancreatic juice and bile.

Thus SIBO can be viewed as a symptom itself. One should always search for factors which could have fostered the occurrence of the disease. A comprehensive list of factors can be found below.

1. Structural/Anatomic

  • Small intestine diverticula
  • Small intestine strictures (radiation, medications, Crohn’s disease)
  • Surgically created blind loops
  • Resection of ileo-cecal valve
  • Fistulas between proximal and distal bowel
  • Gastric resection

2. Motility Disorders

  • Gastroparesis
  • Small bowel dysmotility
  • Celiac disease
  • Chronic intestinal pseudo-obstruction

3. Metabolic Disorders

  • Diabetes
  • Hypochlorhydria (low stomach acidity)

4. The elderly

5. Organ System Dysfunction

  • Cirrhosis
  • Renal failure
  • Pancreatitis
  • Immunodeficiency states
  • Crohn’s disease
  • Celiac disease
  • Malnutrition

6. Medications

  • Recurrent antibiotics
  • Gastric acid suppression

Hypothyroidism has also been associated with SIBO due to it slowing gastrointestinal motility and lowering hydrochloric acid production in the stomach.

It seems the two processes that most commonly predispose to bacterial overgrowth are diminished gastric acid secretion and small intestine dysmotility.


Secretory IgA was mentioned as one of the endogenous defence mechanism. SIgA binds to commensal bacteria and soluble antigens (a molecule capable of inducing an immune response), thereby inhibiting their binding to, and penetrating, the gut lining.

Down modulation of SIgA, which can be caused by chronic stress, can have negative repercussions on intestinal function and integrity. This can take the form of increased adhesion of pathogenic agents (something that causes disease) to the lining of the gut and/or an altered balance of inflammation leading to greater intestinal permeability (Campos-Rodriguez et al., 2013).

Intestinal permeability (leaky gut) has been associated with autoimmune and inflammatory diseases.

Gut homeostasis results from neuro-immune modulation by many different types of molecules including: immune cells and their secretory molecules, neurotransmitters and hormones, all of which influence the generation of intestinal SIgA.

What this means is we need to be considering the state of the nervous and immune systems when considering gut health. Chronic stress significantly effects both the nervous and immune systems (Campos-Rodriguez et al., 2013).

“Stress not only influences SIgA levels [remember this a natural protective mechanism against SIBO] but alters gut motility and slows gastric emptying”  (Kiecolt-Glaser, 2011).

The Migrating Motor Complex (MMC)

The MMC is a mechanical and chemical cleansing of the empty stomach in preparation for the next meal. When the MMC kicks in, there is an increase in gastric, biliary and pancreatic secretions (stomach secretions, bile and digestive enzymes). This helps move the left over matter in the small intestine into the large intestine. Impaired MMC activity may cause retention of the gastric contents and thus cause bacterial overgrowth.

Because the MMC is deactivated when eating, Mark Pimentel, MD, director of the gastrointestinal motility program at Cedars-Sinai Medical Center, suggests:

those prone to small intestine bacterial overgrowth should avoid in-between meal snacking to allow the cleansing wave to adequately divert unwanted waste from the small intestine.

The Migrating Motor Complex is not as active when we sleep, so aiming for an early dinner (allowing at least two hours between eating and going to bed) may be the best approach, certainly for those with SIBO.

The MMC develops approximately every 90–120 minutes to sweep residual debris through the GI
tract. Gastroparesis, a chronic disorder of delayed gastric emptying, can develop secondary to long-standing diabetes, connective tissue disorders, a prior viral infection, and ischemia (an inadequate blood supply to an organ or part of the body).

Prokinetics, substances that support gut motility may be of benefit here (remember gut dysmotility is thought to be a key factor in the development of small intestine bacterial overgrowth). While stress may be a factor in causing dysmotility we obviously want to get improvement in motility as quickly as possible.

Exercise, in some individuals, can be extremely beneficial in supporting gut motility and bowel regularity. Another reason to monitor your day to day activity. Many of our clients notice a difference when increasing their daily step count.

Orocecal Transit Time

OCTT can be defined as how long it takes for food to pass through intestines. It’s important because it influences how efficiently nutrients are absorbed from food and influences fermentation associated with healthy gut flora. Short transit time may be due to inflammation caused by intestinal infection, food allergies, or by absence of healthy intestinal flora. Long transit time is usually due to eating too much refined and processed foods, low thyroid function, dehydration, lack of dietary fiber, serotonin deficiency, lack of exercise and insufficient salt intake. Several other factors affect the orocaecal transit time such as: physiological (age, sex, menstrual cycle), usage of stimulants (coffee, alcohol, cigarette smoking), as well as pathological conditions.

Methylation, Choline & Bile

This is something I go in to more detail in, in the webinar I have created on SIBO (available via the shop). Essentially PEMT (phosphatidylethanolamine methyltransferase) is a gene that is important for the formation of the nutrient phosphatidylcholine (PC). Phosphatidylcholine is the most abundant phospholipid. Phospholipids have a number of very important functions. Some of these include:

  • Component of every cell membrane of the human body
  • Antioxidant properties
  • Brain function, including the formation of many important neurotransmitters such as acetylcholine
  • Liver function – Phospholipids are important for maintaining the balance between other lipids such as triglycerides and cholesterol. Phos. Choline also plays an important role in bile acid production.
  • Methylation reactions – More than half of all methylation reactions involve phospholipids
  • Intestinal health – Phosphatidylcholine protects the intestinal mucosal barrier from inflammation.
  • Growth and development – Phospholipids such as choline are critical for growing infants and children

Choline is abundantly found in many whole foods. This includes: egg yolks, sunflower and flax seeds and other nuts and seeds, as well as animal sources such as liver and whole fat dairy products. Another consideration, if it’s determined one has a greater need for phosphatidylcholine, is using whole lecithin.

Remember bile is one of the endogenous protective mechanisms due to its bacteiostatic properties

Methylation is important in choline production!

This podcast (start around 24 minutes in) discusses the liver, methylation, choline and it’s role in SIBO: Click here.

Food Poisoning

Dr. Siebecker has stated that the most common cause of SIBO is food poisoning.


In addition, certain medications are associated with stasis and SIBO.

For example, narcotics cause intestinal slowing and proton pump inhibitors (PPIs) reduce acid, which can lead to oral microbe penetration of the proximal gut (Pimental & Sachdev., 2013)

Inflammation & Oxidative Stress

A conclusion of a paper published in 2014 stated: “This study indicates that increase in cytokines and decrease in anti-oxidants in UC patients would have resulted in oxidative stress causing delayed GI motility leading to SIBO” (Raana et al., 2014)

Small Intestine Bacterial Overgrowth: Conclusions

In summary SIBO seems to be potentially quite a prominent underlying cause, and consequence, of many diseases, both of the gastrointestinal tract and systemically.

It is important to both consider confirming small intestine bacterial overgrowth, via testing, as well as exploring the underlying causes of the condition. This will allow for a more personalised approach that will increase the likelihood of long term resolution, rather than an approach simply orientated at the eradication of the bacterial overgrowth. While this may improve symptoms in the short term, you risk a return of the overgrowth, and thus symptoms, due to not resolving the initial cause.

Remember, we have endogenous protective factors to protect against small intestine bacterial overgrowth that can be disturbed (as listed and discussed above) and we have extrinsic factors that alter the gut microbiome that influence the development of SIBO which may include: FODMAPs, motility agents, fibre, pre- and probiotics and antibiotics (Chedid et al., 2014).