Small Intestinal Bacterial Overgrowth (SIBO) – Causes and Prevention.


Small intestinal bacterial overgrowth (SIBO) is defined as the presence of excessive bacteria in the small intestine. SIBO is frequently implicated as the cause of chronic diarrhea and malabsorption. Patients with SIBO may also suffer from unintentional weight loss, nutritional deficiencies, and osteoporosis. A common misconception is that SIBO affects only a limited number of patients, such as those with an anatomic abnormality of the upper gastrointestinal (GI) tract or those with a motility disorder.


  • The prevalence of SIBO in the general population is unknown but estimated to be 0–35% in healthy individuals.
  • Anywhere from 30% to 85% of adult patients with IBS are estimated to have SIBO, with the most current data reporting 67% as determined by duodenal aspiration and culture.
  • Two meta-analyses have shown 3.5–9.6 fold increased odds of SIBO in patients with IBS.
  • In the United States and Europe, one in five school-aged children have been diagnosed with abdominal pain-related functional gastrointestinal disorders, including IBS and functional abdominal pain; SIBO has been shown to occur in 34% of pediatric IBS patients.
  • A 2015 study demonstrated that 63% of children aged 4–17 years who were hospitalized for abdominal pain had SIBO.


  • SIBO develops when the normal homeostatic mechanisms that control enteric bacterial populations are disrupted.
  • The two processes that most commonly predispose to bacterial overgrowth are diminished gastric acid secretion and small intestine dysmotility.
  • Disturbances in gut immune function and anatomical abnormalities of the GI tract also increase the likelihood of developing SIBO.
  • Once present, bacterial overgrowth may induce an inflammatory response in the intestinal mucosa, further exacerbating the typical symptoms of SIBO.
  • Although not universally seen, overgrowth of small bowel intestinal flora may result in microscopic mucosal inflammation.
  • Analysis of small bowel biopsies in elderly patients with bacterial overgrowth revealed blunting of the intestinal villi, thinning of the mucosa and crypts, and increased intraepithelial lymphocytes, all of which reversed with antibiotic treatment.

Schematic illustration of small bowel intestinal overgrowth

Risk factors of small intestinal bacterial overgrowth

Some of the risk factors that may cause SIBO:

  • Normal aging
  • Irritable Bowel Syndrome
  • Organ system dysfunction, including cirrhosis, renal failure, pancreatitis, and Crohn’s disease (a chronic inflammatory bowel disease that affects the lining of the digestive tract)
  • Medications such as recurrent antibiotics and those involved in the suppression of gastric acid
  • Motility disorders such as Celiac disease and Gastroparesis (a condition that affects the stomach muscles and prevents proper stomach emptying)
  • Metabolic disorders such as Diabetes and Hypochlorhydria (a lack of stomach acid)
  • Structural anatomic conditions such as Small Intestine Diverticula (a condition in which small, bulging pouches develop in the digestive tract)


The cause of the SIBO is unknown but there is a number of things that cause SIBO. The most common include previous food poisoning (gastroenteritis), medications (proton pump inhibitors, opiates, and antibiotics), abdominal surgery, and certain medical conditions such as follows:

Decreased gut motility: The slower food moves through your gut, the more easily bacteria in the colon will be able to crawl upstream, as it were. At least that’s one theory. I will certainly say patients who have gastroparesis often also have SIBO. I also see this in patients who have had bowel surgeries.

Hypothyroidism will also slow down bowel transit and that can be a predisposing factor.

Wiping out the good guys: Your microbiome is the immune system of your gut, and it is your first line of defense against both pathogenic and opportunistic bacteria that can cause you problems. Lots of antibiotics will lead to flora imbalance (dysbiosis). Proton Pump Inhibitors (PPIs) are actually antifungals, and these can do it too.

Stress:  I know, I know: stress causes everything. And it’s true: whatever your weak link is, is likely to snap when you’re under a lot of stress. But specifically, stress means you’re in “fight-or-flight” mode, and that means less blood flow to your gut (i.e. decreased release of pancreatic enzymes and HCl and bile to help you break down your food, and decreased gut motility) while it instead sends blood to your limbs to help you fight or flee from the perceived danger. So, stress can lead to decreased gut motility, which can mean bacteria might have more of an opportunity to crawl upstream.


Some of the common symptoms of SIBO are as follows

  • Abdominal pain and cramping
  • Bloating and abdominal distension
  • Diarrhea and/or constipation. (May alternate between the two or have one or the other.)
  • Excessive gas (may smell like sulfur or ammonia)
  • Excessive belching (may also smell like sulfur)
  • Feeling full after just a few bites
  • Nausea
  • Heartburn
  • Acid reflux
  • Headaches or migraines
  • Joint and muscle pain
  • Fatigue and/or weakness
  • Steatorrhea (excess fat in stool)
  • Histamine Intolerance

Complications of small intestinal bacterial overgrowth

Severe cases lead to malnutrition. Other possible complications include:

  • Dehydration
  • Excess bleeding due to vitamin deficiency
  • Liver disease
  • Osteomalacia or osteoporosis

Diagnosis and test

Breath Test: This is the gold standard, however, it’s quite cumbersome. Individuals must fast for 12 hours, breathe into a small balloon, ingest a precise amount of sugar, and repeat breath samples every 15 minutes for 3 or more hours. Abnormal breath tests can also signify pancreatic insufficiency and celiac disease.

Easily affordable breath tests for small intestine bacterial overgrowth

Organix Dysbiosis Test: This functional medicine lab tests the urine for by-products of yeast or bacteria in the small intestine. If your small intestine is housing a yeast or bacterial overgrowth, byproducts will appear in your urine, indicating their presence. This test is much easier for patients and only requires one single urine specimen. This is the test I use most often in my clinic.

Comprehensive Stool Test: This is also a functional medicine lab test looking at the flora of the large intestines. If I see all elevated levels of good bacteria, I suspect SIBO.

History: By listening to the patient’s history and symptoms, I’m often able to make a diagnosis.

Treatment and medications

The treatment for SIBO includes controlling and treating any underlying associated illness. The goal is to control the symptoms of small intestine bacterial overgrowth since it may not be possible to “cure” the disease.

Antibiotics are one of the treatments that are helpful in controlling the excess bacteria. It is important that not all the bacteria in the intestine are eradicated since some are required to help with normal digestion.

Amoxillin-clavulanate (Augmentin) and rifaxamin (Xifaxan) are the two common first-line antibiotics that may be prescribed. Depending upon the situation, other antibiotics may also be considered, including:

  • Clindamycin
  • Metronidazole (Flagyl)
  • Floxins (ciprofloxacin [Cipro, Cipro XR, Proquin XR]
  • Levofloxacin [Levaquin])
  • Trimethoprim-sulfamethoxazole (Bactrim, Septra)

While a single course of antibiotics for 1-2 weeks may be sufficient, SIBO has a tendency to relapse, and sometimes repeated courses of antibiotics may be required. In some people, the antibiotics will be routinely cycled, meaning that they will alternate  1-2 weeks on the antibiotic with 1-2 weeks off.

In addition, underlying vitamin and nutrient deficiencies due to malabsorption should be treated.

Prevention of small intestinal bacterial overgrowth

  • Diet –Limiting fermentable carbohydrates and following a diet such as the low FODMAP diet
  • Prokinetics such as Resolor (prucalopride) can help in optimizing gut motility and preventing SIBO relapse
  • Herbal therapies such as iberogast
  • Digestive and pancreatic enzymes therapies may also be used

If the above methods fail, an elemental diet may be tried

  • This is a diet that consists of a liquid formula of pre-digested carbohydrates, proteins, and fats.
  • As a result, the nutrients are absorbed more quickly and can help prevent bacterial overgrowth by quickly eliminating the “fuel” bacteria need to replicate.
  • This is normally done under the supervision of a dietician.
  • Patients may stay on the liquid diet for up to 3 weeks.


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  3. LeeAnne Hollie

    very helpful to help our little one ! u all are the best….. Love u all always & forevermore ?‍?‍?‍??



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  5. Please for someone who usually have periodic stomach ache which is very painful between the beginning of the 5th month (May) in every year; please what could be the possible solution for this painful stomach ache and what may really be the cause?

  6. please help me. I dread eating as it incontrolibe way out of control. do not like eating much. wind to much. I hope you got my other one sent just now. been like this for years. Afraid to eat to much. about 50 when it started in a small way. help me please. it was good to read this. this is me just as I am concerned that you can help me.

  7. This is the best chat ever had about this problem. Dr. knows nothing said. I need help. thank you. please do not print this. inbaristedment.

  8. akinlolu Ayodele

    how can I get treated from sibo

  9. Gabriel Sosanya

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  10. Evans Onsase Loketo

    I’m able to treat myself without any assistance from the doctor. Thank you so much for your help.

  11. I like the app. I would appreciate if there was a possibility for on line QA

  12. Sir,I would like to know that last six months I’m feel with excessive gas problem, Is SIBO could be the reason for that?please tell

  13. all those symptoms I have them but what is the best remedy

  14. Mathapelo Mosiea

    I have stomach gramps everyday I don’t know what to do and its been years now I tried to go to the clinic but they didn’t help me. please help me what is the problem?

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