Gut Flora

The digestive tract contains trillions of bacteria. Bacteria are very small organisms (microbes). There are over 1000 different kinds known to live in the gut. Most bacteria are in the large intestine (colon) where they achieve concentrations of several billion. These “normal” bacteria have important functions in life:

  • They protect against infection by “bad”, or pathogenic, bacteria
  • They help the immune system of the gut to develop
  • They produce a variety of substances, including some essential vitamins, that have an important nutritional value
  • Together, the normal bacteria are often referred to as the gut flora.

Research is currently showing that the composition of these bacteria may affect various aspects of health and disease. A variety of factors may disturb the mutually beneficial relationship between the flora and its host (our bodies), and disease may result. Additionally, some bacteria can cause infection. These are called pathogens.

Video: A Role for Probiotics in Treating IBS?


There is some evidence that certain probiotics may help improve irritable bowel syndrome (IBS) symptoms. Probiotics are generally defined as living microorganisms that, in adequate amounts, provide health benefits.

These are usually bacteria. These bacteria are different from the bacteria that are known to cause illness.

Probiotics can regulate bowel function including motility, sensation, and immune function. They come in many different forms, such as liquid or pills, and can be single or in combination. Some yeasts may have probiotic effects and the effects of dead bacteria are being studied. Most of the studies that have examined the benefit in IBS are small and of low quality.

In some people, changing the kind of gut bacteria with probiotics may make symptoms of IBS better.

The probiotic that, to date, has been studied in high quality studies and has been shown to improve the symptoms in IBS is Bifidobacterium infantis. Recent reviews of all of the probiotic studies have concluded that Bifidobacteria appear to have a beneficial effect in IBS. The symptoms that have shown more consistent improvement with probiotics are gas and bloating.

While you are taking a probiotic, you should observe your symptoms and perhaps keep a log of your progress. This will help you to notice, over the course of several weeks, if the probiotic you are taking is right for you.

Learn more about probiotics and functional GI symptoms


There is also a potential role for some “bad” bacteria residing in the gut to be associated with IBS symptoms in some people. Recent clinical trials have shown that antibiotics, which reduce or alter the bacteria in the gut, may relieve the symptoms of IBS.

Antibiotics can change the balance of the number and kind of gut bacteria. Changing the normal balance may put some people at risk for IBS. On the other hand, if there are too many or the wrong kinds of bacteria in the small intestine, antibiotics may make IBS symptoms better.

Xifaxan (Rifaximin) is one antibiotic (approved by the U.S. Food and Drug Administration in May 2015) for treatment of IBS. In studies it has been found to improve IBS symptoms of abdominal pain and stool consistency in some people after a 10–14 day course of treatment. It is only slightly absorbed in the gut and is generally tolerated well.

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Gut Flora and IBS

The exact role bacteria may have in IBS is still not known. Whether or not these effects come about through subtle and perhaps localized changes in the number or type of bacteria in the colon and/or small intestine, it is evident that manipulation of the flora, whether through the administration of antibiotics or probiotics, deserves further attention in IBS. More medical research is needed.

Learn more about the role of gut bacteria in IBS

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IFFGD is a nonprofit education and research organization. Our mission is to inform, assist, and support people affected by gastrointestinal disorders.

Our original content is authored specifically for IFFGD readers, in response to your questions and concerns.

If you found this article helpful, please consider supporting IFFGD with a small tax- deductible donation.

Adapted from IFFGD Publication #101 revised and updated by Douglas A. Drossman, MD, Drossman Gastroenterology PLLC, Chapel Hill, NC and IFFGD Publication #168 by Tony Lembo, MD and Rebecca Rink, MS, Division of Gastroenterology, Beth Israel Deaconess Medical Center, Boston, MA.

Last modified on July 28, 2015 at 04:26:02 PM



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