Root Causes of SIBO

Small intestine bacterial overgrowth (SIBO) is exactly like it sounds: an overgrowth of bacteria in the small intestine. To understand SIBO fundamentals, please read this post first. Here, we will dive deeper into SIBO to discuss the root causes. Because here is an often overlooked truth in SIBO treatment:

SIBO is a symptom.

While SIBO can cause many symptoms and may lead to other health conditions, SIBO did not just randomly happen. The bacteria grew in your small intestine for a reason and for successful treatment, you need to address the cause. Otherwise, SIBO will recur. Recurrence happens within 9 months in up to 44% of patients treated with antibiotics because most doctors don’t address the cause. I have noticed that most MDs treat with antibiotics until a negative breath test is achieved and offer no further treatment. Other doctors are aware that recurrence is an issue so they advise long term use of the low FODMAP diet (which quite frankly sucks for the patient) or use of motility agents (pharmaceutical or natural). But most fail to address the true root cause so most patients continue to struggle with SIBO.

root causes of sibo

Impaired Digestive motility

Basically, if your food moves slowly through your digestive tract, you are more at risk of SIBO. So what can cause slow motility?

  • autoimmune attack on the muscle of your intestine, usually triggered by food poisoning

  • traumatic brain injury (common in people playing contact sports or in motor vehicle accidents)

  • hypothyroidism

  • chronic infections like EBV, lyme or lyme coinfections

  • diabetes (high blood sugar damages nervous system)

  • mold toxicity

  • issues with connective tissue (Ehlers Danlos Syndrome, Scleroderma, POTS)

  • mast cell activation syndrome

  • adhesions and connective tissue restrictions from abdominal surgery

  • endometriosis

  • ileocecal valve dysfunction

Impaired digestive function

Your stomach acid, bile, and pancreatic enzymes all work to create an environment that is not friendly to bacteria. So any digestive deficiency can cause SIBO.

  • low stomach acid (usually due to stress or H. pylori)

  • bile deficiency (can be due to liver detoxification issues, excess hormones, methylation issues, SNPs in certain genes like MTHFR)

  • low pancreatic enzymes (can be due to stress or H. pylori)

  • deficiency in brush border enzymes (can be due to celiac disease or other inflammatory conditions of the small intestine)

  • secretory IgA deficiency (can be due to general immune dysfunction, chronic infections, stress)


Some medications are known to lead to SIBO, some through the above mechanisms.

  • proton pump inhibitors (Prilosec)

  • narcotics/opioids

  • cholestyramine

  • frequent antibiotic use

  • antispasmodics (dicyclomine, hyoscyamine, loperamide, promethazine)

  • tricyclic antidepressants (amitriptyline and others)

New SIBO Treatment Paradigm

  1. Treat SIBO by eradication bacteria from small intestine.

  2. Treat the root cause of the overgrowth.

For many people, there may be a combination of root causes that need to be addressed. For most people, stress very much impacts their digestion leading to some of the above causes (low stomach acid, low secretory IgA, etc), so managing stress and following proper eating hygiene can go a long way to prevent recurrence.


  • Dukowicz AC, Lacy BE, Levine GM. Small intestinal bacterial overgrowth: a comprehensive review. Gastroenterol Hepatol (N Y). 2007;3(2):112-22.

  • Bures J, Cyrany J, Kohoutova D, et al. Small intestinal bacterial overgrowth syndrome. World J Gastroenterol. 2010;16(24):2978-90.

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I'm Dr. Carly and my mission is to create a health revolution. I believe that another prescription is not the answer. I believe in using natural therapies that go beyond the symptoms. And I believe that doctors should spend way more than 7 minutes with a patient.