Gut microbiome (or microbiota) refer to the ~ 500 types of probiotics found in the human gut.

No current guidelines exist for using probiotic or prebiotic supplements for those with celiac disease. However, using either supplemental or dietary probiotics can help decrease the risk of dysbiosis.

  • The right probiotic or symbiotic can improve digestive symptoms like gas, bloating, diarrhea or constipation often within a few doses.
  • Probiotic supplements are either single specific strains of bacteria, or multi strain, containing sometimes dozens of different types of organisms.
  • Symbiotics are supplements that contain both probiotics and prebiotics. Most often this is the rice extract, fructooligosaccharide (FOS). Some people who are fructose intolerant can have a negative reaction to these prebiotics.
  • Probiotic supplements are either shelf stable, meaning they do not require refrigeration, or heat sensitive. Make sure to store your supplements appropriately to keep the probiotics effective. Don’t heat or cook with probiotics; the heat will distort them.
  • Probiotic supplements tend to have a fairly short shelf life, regardless of whether they are refrigerated or shelf stable. If the expiration date has passed, the probiotics are likely not effective anymore.
  • Many probiotic strains are initially cultured in a dairy based medium. The amount of dairy left in the pills can vary widely, so if you don’t tolerate dairy well (lactose intolerance), make sure you are getting a dairy-free version.
  • There are many different supplemental forms of probiotics supplements including powders, pills, coated straws and chewables.
  • Most probiotic supplements are measured in Colony Forming Units (CFU), which tells you how many active bacteria are in the supplement. Some companies list in milligrams (mg), which doesn’t tell you how many probiotics are in their supplements and prevents effective comparison between brands.
  • Probiotics are non-toxic even at high doses. People can tolerate and benefit from hundreds of billions of probiotics daily. The strongest probiotic on the market currently has 900 billion bacteria per dose. Talk to your doctor or dietitian to determine the best dose for you if you are started on a probiotic.
  • Even though probiotics are non-toxic, people can have negative reactions to certain strains of bacteria. Which probiotic people may have a reaction to varies from one person to another.
  • Fecal transplants, where feces from a healthy person are transplanted into the colon of an ill person, are a controversial way to treat dysbiosis. This method is found to be effective for treating a dangerous bacterial infection in the gut called C. difficile. 1


  • Having a consistent source of prebiotics and probiotics is thought to be important for preventing and/or treating several diseases, providing health benefits, and regulating the immune system. This can come from food and/or supplements.
  • When choosing a probiotic supplement, consider the strain of bacteria, the strength of the supplement, appropriate storage, and the expiration date.
  • If you are intolerant of dairy products, make sure your probiotic is dairy-free as well as gluten-free.
  • Probiotic supplements are non-toxic, but individual reactions to specific strains can vary widely. Severe reactions are very rare. It seems that people have an affinity to specific strains. There is no practical test that can determine which strains are most beneficial for a given individual.
  • If you think you could benefit from a probiotic and/or prebiotic, speak to a qualified health provider. Probiotic supplements are not all equal. A healthcare provider familiar with probiotics can help you sort through the myriad of choices in the market to decide which strain or combination of strains can be helpful to you. Always choose one that is gluten-free.


Noland D, Pugh GF. Balancing Your Gut: Functional Medicine in Celiac Disease. In Real Life with Celiac Disease: Troubleshooting and Thriving Gluten-Free . Eds. Dennis M, Leffler D. AGA Press, Bethesda, MD. 2010.


  1. Hamilton MJ, Weingarden AR, Unno T, Khoruts A, Sadowsky MJ. High-throughput DNA sequence analysis reveals stable engraftment of gut microbiota following transplantation of previously frozen fecal bacteria. Gut Microbes. 2013 Mar 1;4(2):125-35

Revision Date: 5-16-13 
Authors: Christine Doherty, N.D. 
Editors: Melinda Dennis, MS, RD, LDN, Toufic Kabbani MD, MPH

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