7 min|Dr. Maya Kuczma

9 Causes of SIBO That Has You Struggling

Wellness, Health, Gut Health

The Real Deal About SIBO

Small Intestinal Bacteria Overgrowth (SIBO) occurs when there are too many bacteria in the wrong place (the small intestine). Although bacteria is vital for the functioning of the healthy body, too many bacteria or an imbalance of certain types of bacteria can lead to a variety of health concerns (SIBO symptoms).

SIBO does not occur randomly; there are many reasons why bacteria can relocate to the small intestine, or why the bacteria usually present there is able to flourish. In this sense, SIBO is both the cause of a variety of symptoms - and is caused by a variety of health concerns. In order to fully treat SIBO, it is important to identify what caused it. Without treating the cause, SIBO will likely recur after treatment. Typically, levels of bacteria are kept in check by multiple features of the digestive tract:

  • acidic secretions from the stomach
  • downward propulsive impulses (wave-like movements) such as peristalsis and the migrating motor complex (MMC)
  • secretion of bile from the gallbladder
  • immunoglobulins in the small intestine (that fight bacteria and other pathogens)
  • ileocecal valve, a one-way valve connection between the small intestine and large intestine

Dysfunction in any of these processes can allow for bacteria to overgrow in the small intestine, resulting in SIBO.

9 Causes of SIBO

1) Low stomach acid

Low stomach acid, also known as hypochlorhydria, interferes with the initial stages of digestion. Without adequate acid, food is not broken down sufficiently, allowing large undigested carbohydrates into the small intestine. Bacteria feed off of these carbohydrates, allowing them to proliferate. Stomach acid suppresses the growth of bacteria; when levels are low, bacteria are able to proliferate freely.

As a by-product of carbohydrate digestion, the bacteria produce hydrogen gas, increasing pressure in the abdomen, pushing acid from the stomach into the esophagus, leading to 'acid-reflux’(1). Commonly, doctors will prescribe an acid-blocking medication; however, since the initial issue was a lack of acid, these medications can worsen symptoms and increase the likelihood of developing SIBO(2,3). Other factors can lead to low stomach acids, such as the use of antacids, stress, inflammatory foods, nutrient deficiencies, or an H. Pylori infections (4,5).

2) Altered bile flow and enzyme production

Bile and enzymes are both required for adequate digestion of the food we eat (The Gut). Proteolytic enzymes and bile acids additionally have anti-bacterial effects, helping to protect our gut against bacterial overgrowth. Without sufficient enzymes, carbohydrates may not be broken down sufficiently, providing fuel for bacteria to overgrow. Without the protective effects of enzymes and bile acids, there is an increased risk of developing SIBO (7).

3) Stress

Stress interferes with many aspects of digestion. When we are under stress, our body produces less stomach acid, leading to reduced bile secretion and enzyme production, both of which we have just learned can contribute to SIBO. Additionally, stress can weaken the immune system, allowing for overgrowth of bad bacteria or an infection that may require antibiotics, further increasing the risk of developing SIBO. Stress also interferes with gut motility, slowing the movement of food, and bacteria, through the gut. Reduced gut motility predisposes us to develop SIBO.

4) Migrating Motor Complex Dysfunction

If our digestive system is healthy, the migrating motor complex (MMC), a pattern of gut contraction, moves bacteria from the small intestine into the large intestine between meals and during the night. However, if MMC function is impaired, bacteria are not cleared from the small intestine correctly, increasing the likelihood of developing SIBO (Gut Motility). A variety of conditions increase the risk of impaired MMC function, such as:

  • hypothyroidism
  • certain medications such as opioids and proton pump inhibitors
  • inflammatory bowel diseases such as Crohns and Colitis
  • Diabetes
  • Celiac disease
  • gastroenteritis, C difficile and other infections
  • Lyme disease
  • Ehler's Danlos
  • history of eating disorders

5) Dysfunction of intestinal nerves and/or muscles

In addition to the MMC, the digestive tract requires peristalsis to move food from mouth to anus. Many conditions can interfere with this movement including, but not limited to achalasia, gastroparesis, Parkinson’s, scleroderma, and other neurogenic issues (Gut Motility). Additionally, certain medications reduce gut motility such as anticholinergics and opioids (8).

Structural changes in the digestive tract can also inhibit movement of bacteria from the small intestine to the large intestine, or allow migration of bacteria upwards from the large intestine. Adhesions, obstructions, non-draining pockets in the small intestine (diverticuli), ileocecal valve removal or impairment, strictures, and masses can all interfere with normal bacterial flow.

6) Antibiotics

Even though SIBO is a chronic bacterial overgrowth that may be treated with antibiotics, the dysbiotic effects of antibiotics can also cause it. Systemic antibiotic exposure, through prescriptions as well as exposure to antibiotic-treated livestock, kills off both harmful and helpful bacteria, upsetting the balance of the microbiome.

When many of the protective bacteria are killed, other bacteria can proliferate and overgrow, increasing the risk of developing SIBO. Additionally, chronic exposure to antibiotics can lead to drug-resistant bacteria, making SIBO, and other infections, more difficult to treat(9).

7) Dysfunctional immune system

The foundation of our gut microbiome is built in early infancy, during childbirth and breastfeeding. Children who are born via C-section and those who are not breastfed are at greater risk for microbiome imbalances (dysbiosis) such as SIBO(10). Additionally, conditions of immune deficiency, such as HIV/AIDs and IgA deficiency, as well as autoimmune conditions, such as Celiac and scleroderma, predispose to SIBO.

8) Food poisoning

An episode of acute gastroenteritis (food poisoning) can greatly impair the MMC. When we are infected by harmful bacteria during a case of food poisoning, the bacteria release a toxin. Our body, in an effort to fight off the infection, attacks the toxin.

However, certain cells in our intestine that play a role in the MMC look very similar to the toxin; our immune system, attempting to protect us, can also begin to attack these cells, damaging the MMC, leading to bacterial overgrowth(15, 16). One occurrence of gastroenteritis may increase the chances of developing IBS/SIBO six-fold, resulting in post-infectious SIBO(17).

9) Additional Potential Causes

There are many other health concerns under consideration as risk factors for developing SIBO such as carbohydrate intolerance, the location we live in, and leaky gut(18,19,20). Additionally, since the gut is connected to every part of the body, many conditions have been linked to SIBO, such as acne, chronic fatigue syndrome, hypothyroidism, rheumatoid arthritis, and many, many others.

Certain conditions seem to be particularly associated with SIBO such as irritable bowel syndrome (IBS), Ulcerative colitis, Crohn’s disease, and Celiac(21). It is unclear as to whether these conditions predispose people to SIBO, or if SIBO is playing a large role in the pathogenesis of these conditions. What is clear is that testing for SIBO, and treating accordingly, should be explored in a wide variety of conditions.


As we can see from this list, although SIBO can lead to many wide-ranging symptoms throughout the body, it is also the result of specific health concerns. SIBO itself is not the disease; it is the end result. If we simply treat SIBO, we are not addressing the root conditions that allowed SIBO to thrive.

A full treatment plan must address the bacterial overgrowth of the small intestine while also working on the root cause(s) to ensure a complete eradication of SIBO and decrease the chances of recurrence. Treating SIBO: Diet

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  1. https://chriskresser.com/the-hidden-causes-of-heartburn-and-gerd/
  2. https://www.ncbi.nlm.nih.gov/pubmed/8853759/
  3. https://www.ncbi.nlm.nih.gov/pubmed/23270866
  4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC26223/
  5. http://www.sciencedirect.com/science/article/pii/S0016508597700751
  6. https://chriskresser.com/more-evidence-to-support-the-theory-that-gerd-is-caused-by-bacterial-overgrowth/
  7. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2890937/
  8. https://www.ncbi.nlm.nih.gov/pubmed/7882635
  9. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378521/
  10. https://www.ncbi.nlm.nih.gov/pubmed/29018787
  11. https://www.omicsonline.org/open-access/small-intestinal-bacterial-overgrowth-sibo-2161-069X.1000225.php?aid=31428#8
  12. https://www.ncbi.nlm.nih.gov/pubmed/1634799
  13. https://www.ncbi.nlm.nih.gov/pubmed/2387510
  14. https://www.ncbi.nlm.nih.gov/pubmed/9890463
  15. https://www.ncbi.nlm.nih.gov/pubmed/25424202
  16. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4430499/
  17. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2721231/
  18. http://pediatrics.aappublications.org/content/49/2/233.short
  19. https://www.hindawi.com/journals/archaea/2014/576249/
  20. http://onlinelibrary.wiley.com/doi/10.1002/hep.22848/full
  21. https://www.siboinfo.com/associated-diseases.html
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