Could Small Intestinal Bacterial Overgrowth be the Cause of your Unexplained GI Symptoms?



Gut bacteria continues to be a hot topic. Experts are often touting foods to increase and improve the microflora in our intestines. But while we want to ensure we have adequate colonies of ‘good’ bacteria in the large intestine (colon), when it comes to the small intestine, bacteria are not so welcome.

The small intestine is only supposed to house a very limited number of bacteria. Sometimes, however, too many bacteria find their way in, causing small intestinal bacterial overgrowth (SIBO). This can result in a host of unpleasant gastrointestinal symptoms as well as long-term damage to the gut if it is not properly treated. So what is SIBO, what causes it, how can you tell if you have it, and what can you do about it?

What is SIBO?

 SIBO is defined as the presence of more than a certain number of bacteria in the small intestine. (1)

What causes SIBO?

There are five major mechanisms that maintain a healthy person’s normal gut microflora and stop bacteria from getting into the small intestine. They are: 

  1. Stomach acid 
  2. Antimicrobial enzymes from the pancreas
  3. Muscle movements of the small intestine (migrating motor complex - waves of electrical activity that ‘sweep’ the intestines during periods of fasting)
  4. Structural integrity of the gastrointestinal tract
  5. The gut immune system (2,3)

When one or more of these mechanisms fails, unwanted bacteria can make their way into the small intestine.

What causes these mechanisms to fail?

There are a number of potential causes. They include:

  1. Reduced gastric acid caused by acid-suppression medications (such as proton pump inhibitors), achlorhydria (low stomach acid), or chronic alcohol use
  2. Reduced pancreatic enzymes as a result of chronic pancreatitis or cirrhosis
  3. Structural defects in the GI tract caused by Crohn’s disease, surgical alterations (such as gastric bypass), or small intestinal diverticulitis
  4. Motility disorders caused by fibromyalgia, celiac disease, diabetic enteropathy, hypothyroidism, chronic narcotic use, and aging (3)

In addition, it is thought that taking antibiotics, contracting a stomach virus, and eating certain foods to which a person is sensitive could lead to an increased risk of SIBO.

What are the symptoms of SIBO?

In some patients, SIBO causes non-specific GI symptoms such as bloating, flatulence, diarrhea, abdominal cramping, nausea, and weight loss. In others, it causes nutrient malabsorption, which can lead to fatty stools, weight loss, and vitamin A, vitamin B12, vitamin D, and vitamin E deficiencies. If left untreated, SIBO can lead to megaloblastic anemia, peripheral neuropathy, night blindness, and even osteoporosis. (4)

How to tell if you have SIBO

If you experience regular unexplained gastrointestinal symptoms, it is worth asking your doctor or a Registered Dietitian Nutritionist to test you for SIBO. The gold standard in testing is culturing a sample of liquid from the small intestine. Unfortunately, however, it is an expensive and invasive procedure. Thankfully, the simpler and noninvasive option of hydrogen and methane breath testing is widely available and still effective at identifying SIBO.

The breath testing involves drinking a sugar solution (usually glucose) and then measuring the gas that the person exhales. If there is an overgrowth of bacteria in the small intestine, those bacteria will consume the sugar and produce hydrogen or methane gas. High levels of those gases in the exhaled air therefore suggest that a person does indeed have SIBO. 

Treatment for SIBO

There are several steps involved in treating SIBO. They are as follows. (5)

(1)  Anti-Microbial Agents

Treatment for SIBO requires the use of antimicrobial agents to modify the intestinal microflora. This usually begins with a course of antibiotics. While there are several broad-spectrum antibiotics that are prescribed for SIBO, they usually come with side effects. Therefore, Rifaximin is often prescribed because it is poorly absorbed in the gut, so its effects stay within the GI tract. (6)

For people who prefer not to take antibiotics, there are herbal therapies available. Studies have shown them to be as effective as antibiotics in treating SIBO. (7)

After completing the course of antibiotics, it is often useful for patients to take herbal anti-fungal medications to ensure that all unwanted microbes are removed from the small intestine.

(2) Management of Symptoms

Once the antimicrobial therapy has been completed, patients need to manage their symptoms by avoiding foods that can contribute to intestinal fermentation. This usually involves following a low FODMAP or specific carbohydrate diet. 

(3) Correct Nutrient Deficiencies

The next step involves correcting any nutrient deficiencies. In particular, vitamin B12, the fat-soluble vitamins A, D & E, omega-3 fatty acids, and iron are the nutrients that are most at risk in SIBO patients.

(4) Repair Intestinal Lining

After the symptoms have subsided, patients can begin to repair their intestinal lining. This involves lowering inflammation by optimizing the omega-3 to omega-6 fatty acid ratio in the diet, and eliminating any problematic foods, such as gluten. In addition, patients can nourish the gut lining by increasing their intake of foods rich in zinc and vitamin A. Some may also benefit from taking an L-glutamine supplement, although this should be discussed with a doctor or dietitian. 

(5) Prevent Recurrence

The final stage of treatment is preventing recurrence. This involves:

  1. Finding and treating the underlying cause
  2. Correcting gut dysbiosis with probiotics
  3. Promoting the migrating motor complex

The first two (finding the cause and correcting dysbiosis) are often difficult and controversial and should be done with the help of a doctor or dietitian. The third, however, can be done by the patient alone. To promote the muscle movements of the small intestine, patients should leave at least 3 to 4 hours between eating. In addition, they should take steps to reduce stress, as it can adversely affect the migrating motor complex.

Bottom Line

If you suffer from unexplained gastrointestinal symptoms such as bloating, excessive flatulence, diarrhea, nausea, or intestinal pain, you might be suffering from SIBO. A simple breath test can be used to diagnose the condition. If you find you do have SIBO, it is very treatable. However, the treatment process can be long and convoluted. If you need help, you can work with your doctor and a Registered Dietitian Nutritionist to eliminate the SIBO, repair your intestinal lining, and prevent recurrence. If you have any questions, please feel free to email us here at Pacific Nutrition Partners. 


1 - Dukowicz AC, Lacy BE, Levine GM. Small intestinal bacterial overgrowth: a comprehensive review. Gastroenterology & hepatology. 2007;3(2), 112.

2 - Quigley EM, Abu-Shanab A. Small intestinal bacterial overgrowth. Infect Dis Clin North Am. 2010;24:943–959 (viii-ix)

3 - Iturrino J, Grover M. Small‐Intestinal Bacterial Overgrowth. Practical Gastroenterology and Hepatology Board Review Toolkit. 2016;285-290. 

4 - Saad RJ, Chey WD. Breath testing for small intestinal bacterial overgrowth: maximizing test accuracy. Clinical Gastroenterology and Hepatology. 2014;12(12), 1964-1972.

5 - Jacob A. Treatment and Management of SIBO – Taking a Dietary Approach Can Control Intestinal Fermentation and Inflammation. Today’s Dietitian. 2012;(14), 16. Retrieved from

6 - Gatta L, Scarpignato C, McCallum RW, Lombardo L, Pimentel M, D'Incà R, ... Cerda E. Systematic review with meta‐analysis: rifaximin is effective and safe for the treatment of small intestine bacterial overgrowth. Alimentary pharmacology & therapeutics. 2017;45(5), 604-616.

7 - Chedid V, Dhalla S, Clarke JO, Roland BC, Dunbar KB, Koh J, ... Mullin GE. Herbal therapy is equivalent to rifaximin for the treatment of small intestinal bacterial overgrowth. Global advances in health and medicine. 2014;3(3), 16-24.