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& Inflammatory Bowel Disease (IBD)



  • There are more microbe cells (bacteria, fungi, or protozoa) in our body than human cells.  These microbes are essential in functions such as digestion of food and our defenses against harmful microbes.  One theory about IBD is that there is a change in the balance of healthy and unhealthy microbes in the gut that triggers abnormal inflammation.  This is an area of much research interest but there is not yet enough information to draw clear conclusions. 

  • Antibiotics are medicines used in the treatment and prevention of bacterial infection.   They may either kill or inhibit the growth of bacteria. Their use requires a prescription.

  • Antibiotic use has been clearly associated with developing IBD.  Children with IBD are more likely to have received antibiotics in the years before the development of IBD than children without IBD. This is also true for adults. It has not been shown that any specific class of antibiotics is at issue.  One possibility is that the use of antibiotics has an influence on the microbes in the gut.

  • In spite of this finding, antibiotics are important and helpful in the treatment of IBD when people have specific infections or the risk of infection.

  • There is no evidence that antibiotic therapy is beneficial for most people with ulcerative colitis. 

  • There is some evidence that some antibiotics may benefit Crohn’s disease especially in treating fistulas that occur around the anus or in preventing disease recurrence after surgery


  • Metronidazole (also known as Flagyl) and ciprofloxacin are the most commonly prescribed antibiotics in the treatment of IBD.  These antibiotics may be used by themselves or in combination.  These medicines are also used in people without IBD.

  • A fistula is an abnormal connection (a tube) between from one organ to another.  In Crohn’s disease fistulas can develop between the bowel and other parts of the abdomen.  Metronidazole and ciprofloxacin are prescribed in the treatment of active fistulas around the abdomen or anus.  In clinical trials evaluating the use of antibiotics in treating anal fistulas only about 1 in 5 persons benefitted, but these studies were very small. In usual practice in about 1 in 2 patients with fistulas, antibiotics can help close them. However, it is not uncommon that once the antibiotics are stopped the fistulas open up again.

  • Metronidazole may be prescribed in persons with Crohn’s disease who have had a part of their bowel removed, especially if the surgery involved removing a segment of their ileum (the end of their small bowel) in order to prevent disease recurrence.

  • Pouchitis is inflammation in the ileal pouch created after the colon is removed for colitis.   Metronidazole and ciprofloxacin are prescribed to treat pouchitis.  In usual practice about 1 in 2 or half of patients who have pouchitis, antibiotics can resolve the symptoms. However, occasionally patients need to remain on antibiotics continuously to control the pouchitis.

  • Sometimes patients find that antibiotics are initially effective in treating their fistulas or pouchitis and then they stop working and need to use different treatment approaches.

  • Other antibiotics may be prescribed to treat infections that arise in persons with Crohn’s disease or ulcerative colitis.

  • Antibiotics are given most of the time as pills taken between one and three times per day.  When patients are ill enough that they need to be hospitalized the antibiotics may be given by intravenous infusion (infused directly into a vein in the arm).

  • Some patients get prescribed antibiotics to treat their Crohn’s disease even if no fistulas are present. There are no published studies that support the effectiveness of antibiotics to treat intestinal inflammatory disease in Crohn’s disease

  • If patients with severely active ulcerative colitis are admitted to hospital and have fever sometimes they are treated with intravenous antibiotics.


Side effects and interactions

  • Common side effects of antibiotics are diarrhea, bloating, and nausea - these are often mild and typically stop when the antibiotics are discontinued.

  • Clostridioides difficile (abbreviated as C. Difficile) is a bacteria that can cause serious infections when people are being treated with an antibiotic. When a person taking antibiotics develops bloody diarrhea while taking the antibiotic or even up to several weeks after taking the antibiotic, the stool should be tested for C. Difficile.  This infection is extremely rare after using metronidazole (Flagyl) and this antibiotic is an effective treatment of Clostridium difficile infection.

  • Yeast infections can occur during chronic antibiotic use. This can manifest as oral thrush, esophageal symptoms (such as difficulty swallowing) or for women vaginal itching or burning.

  • Allergic reactions may be caused by antibiotics.  These may include rashes, itching, or even in rare cases, joint pains and swelling of the face, neck or hands. If a person is found to be allergic to an antibiotic he/she should not receive that antibiotic again or antibiotics that are considered part of the same class. Note that getting diarrhea or nausea while using an antibiotic is not an considered to be an allergy, and therefore it would be safe to receive that antibiotic again in the future if it was necessary

  • Metronidazole can cause numbness and tingling in the hands or feet. When this occurs the drug should be stopped and for nearly all persons these symptoms will disappear.

  • Ciprofloxacin can sometimes cause problems with tendons or joints. If pain in the joints arises when ciprofloxacin is taken you should notify your doctor.

  • Drug interactions.  Antibiotics can sometimes interact with other drugs. The metabolism or break down of the antibiotics can sometimes interfere with the metabolism and drug levels in the body of other drugs. Patients should discuss with their doctor or pharmacist if the antibiotics they are prescribed could interact with any other drugs they are using. Metronidazole is one antibiotic that rarely causes problems when used with other drugs. It is generally very safe.

  • Pregnancy and breastfeeding.  Metronidazole can be taken in pregnancy and when breastfeeding.  Ciprofloxacin is often not used in the first trimester of pregnancy or when breastfeeding



Bernstein CN, Burchill C, Targownik LE, Singh H, Roos LL. Events Within the First Year of Life, but Not the Neonatal Period, Affect Risk for Later Development of Inflammatory Bowel Diseases. Gastroenterology. 2019 Jun;156(8):2190-2197.

Bernstein CN. Treatment of IBD: Where we are and where we are going. American Journal of Gastroenterology 2015; 110:114-126.


Khan KJ, Ullman TA, Ford AC, et al. Antibiotic therapy in inflammatory bowel disease: a systematic review and meta-analysis. American Journal of Gastroenterology 2011;106(4): 661-73.


Last reviewed: March 2020

For more information and fact sheets about IBD and its treatment please visit:


Disclaimer: This information is provided for educational purposes only. Always consult a qualified health care professional for your specific care.

Source: This summary provides scientifically accurate information.  It was prepared in a research review by researchers with the IBD Clinical and Research Centre, University of Manitoba with assistance from colleagues in Canada and internationally. 


Acknowledgement:  Preparation of this material was supported by funding from the Canadian Institutes of Health Research. 

©2016 Charles N. Bernstein, John R. Walker on behalf of Manitoba IBD Clinical and Research Centre. This work is licensed under a Creative Commons Attribution-nonCommercial-NoDerivs 2.5 Canada License.  You are free to copy and distribute this material in its entirety as long as: 1) this material is not used in any way that suggests we endorse you or your use of the material, 2) this material is not used for commercial purposes, 3) this material is not altered in any way (no derivative works). View full license at

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