Merck Manual

Please confirm that you are not located inside the Russian Federation


Bacterial Overgrowth Syndrome


Atenodoro R. Ruiz, Jr.

, MD, The Medical City, Pasig City, Metro-Manila, Philippines

Last full review/revision Oct 2019| Content last modified Oct 2019
Click here for the Professional Version

Bacterial overgrowth syndrome is a disorder in which poor movement of intestinal contents allows certain normal intestinal bacteria to grow excessively, causing diarrhea and poor absorption of nutrients (malabsorption).

  • Some conditions and disorders slow or stop the movement of contents through the intestines.

  • Some people have no symptoms, whereas others have abdominal discomfort, diarrhea, bloating, and excessive flatulence.

  • The diagnosis is based on symptoms, particularly in people who have had certain types of surgery or have certain disorders.

  • Antibiotics can eliminate the excess bacteria.


The normal steady movement of intestinal contents (peristalsis) is important to help maintain a proper balance of bacteria in the small intestine. Conditions in which intestinal contents slow or pool in one place allow excess bacteria to grow. Such conditions include certain types of surgery on the stomach, intestines, or both. Disorders such as diabetes, systemic sclerosis, and amyloidosis also can slow peristalsis, causing bacterial overgrowth.

The excess bacteria consume nutrients, including carbohydrates and vitamin B12, leading to lower calorie intake and vitamin B12 deficiency. The bacteria also split bile salts, which are secreted by the liver to aid digestion. The loss of bile salts causes difficulty absorbing fats, leading to diarrhea and poor nutrition.


The most frequent symptoms of bacterial overgrowth syndrome are abdominal discomfort, diarrhea, bloating, and excess flatulence. Some people have few symptoms or only weight loss or nutritional deficiencies. Other people have severe diarrhea or steatorrhea (light-colored, soft, bulky, greasy, and unusually foul-smelling stool).


  • A doctor's evaluation of symptoms

  • Breath tests and stool culture

  • X-rays

Doctors base the diagnosis on typical symptoms, particularly in people who have had certain types of surgery or have certain disorders.

Sometimes they take a fluid sample from a flexible tube inserted into the small intestine in a procedure called endoscopy. Doctors culture the fluid to determine how many bacteria are present.

Often doctors instead do breath tests, such as the 14C-xylose breath test. In this test, the person drinks a liquid containing a special, faintly radioactive marker (carbon-14) attached to a sugar (xylose). If the 14C-xylose is broken down by the excess bacteria, the carbon-14 can be detected in the person’s breath, which suggests the person has bacterial overgrowth.

Sometimes people have abnormalities of their internal structures that make them susceptible to bacterial overgrowth. To identify these abnormalities, doctors take x-rays of the stomach and small intestines after a person drinks a liquid that shows up on x-rays (called an upper gastrointestinal [GI] series).


  • Antibiotics

  • Changes in diet

Most people get better with antibiotics given by mouth for 10 to 14 days.

Because the excess bacteria grow faster with carbohydrates, people should eat a diet higher in fat and lower in carbohydrates and fiber. Doctors prescribe supplements to correct any nutritional deficiencies.

NOTE: This is the Consumer Version. DOCTORS: Click here for the Professional Version
Click here for the Professional Version
Others also read

Also of Interest


iOS Android
iOS Android
iOS Android