Small intestinal bacterial overgrowth (SIBO): when your microbiome moves north & gets out of control

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Bloating, gas, abdominal discomfort, diarrhea… who doesn’t experience those pesky symptoms from time to time. Could it be IBS? Possibly—but up to 84% of patients who met IBS diagnostic criteria actually had small intestinal bacterial overgrowth (SIBO). SIBO is when the bugs from your colon makes their way up to your small intestine therefore taking up a lot more space to digest and ferment food and create tons of gas and bloating.

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Adapted from JAMA

Adapted from JAMA

When we talk about the microbiome, we are mostly referring to the bugs that live in the very end of your small intestine and colon. There are very few bugs in your stomach or duodenum (1st portion of your small bowel) due to acidity and peristalsis. Then there are 10,000 aerobes in the mid-distal jejunum, 10^9 (1 billion) mixed bugs in the terminal ileum, and 10^12 (1 trillion) anaerobes in the colon. In SIBO, due to certain risk factors, there is backward movement of these bugs up the GI tract where they're not supposed to be, causing inflammation like colitis that can even mimic a Crohn’s flare.

What are the risk factors for SIBO?

  • Functional/motility disorders: IBS, opiate use, radiation, scleroderma, diabetes
  • Altered anatomy: adhesions/scar tissue from previous surgery, radiation, Crohn’s/Ulcerative Colitis, small bowel tumors, small bowel diverticulosis,  gastric bypass surgery
  • Pancreas problems and cirrhosis change the composition of digestive enzymes and bile, allowing microbes to grow
  • Immune disorders: IgA deficiency, HIV
  • Low gastric acid levels, often seen with chronic anti-acid use

As usual, the key is PREVENTION!

  • Avoid opiates/narcotics, benzodiazepines and other drugs that slow down your gut
  • Avoid chronic anti-acid use (nexium, Prilosec, etc)- If you need it, discuss the appropriate dose and duration with your doctor
  • Have good control of your diabetes and Crohn’s/Ulcerative Colitis if you have it

How is it diagnosed?

Adapted from JAMA

Adapted from JAMA

  • Hydrogen and methane breath tests: when one eats a carb such as glucose, your gut bugs process it and produce hydrogen or methane. Usually this happens way down your GI tract, but if you have an overgrowth of bacteria in your small intestine then you can detect increased amounts of hydrogen and methane in your breath
  • Labs: Anemia with decreased vitamin B12, low protein and fat-soluble vitamins, Increased folate, increased fat in your stool signifying malabsorption

**After diagnosis: make sure your doc investigates WHY you got SIBO. For example, endoscopy may be necessary to look for Crohn’s disease of the upper GI tract.


  • 1st, treat the underlying disease. Ex. For slow GI motility,  discuss a pro-kinetic (reglan, erythromycin) or a pro-peristaltic drugs (octreotide) with your doctor
  • DIET! A high-fat, low-carbohydrate, low-fiber, dairy-free diet is key.
    • Carbs are the main nutritional source for bacteria, so diets should be low-carb.
    • Fat is not metabolized by bacteria therefore may lessen production of gas, bloating, discomfort.
    • Lactase deficiency develops in many patients with SIBO, so get tested for lactose intolerance with a breath test and avoid dairy if positive
  •  ANTIBIOTICS: Most patients need treatment with antibiotics to reduce the troublesome gut flora, at least 7-10 days but may require months or repeated treatments. Rifaximin (1650 mg/day), a nonabsorbable antibiotic, may be 1st choice as there is less clinical resistance.
  • Prebiotics & probiotics may be helpful but evidence is limited and therefore use as primary treatment is not recommended

It's more common than you (or your doctor) may think! Always get to the bottom of your symptoms!

#loveyourgut. #listentoyourgut.