Reviewed by: HU Medical Review Board | Last reviewed: August 2023

People with inflammatory bowel diseases (IBD) like Crohn’s disease (CD) and ulcerative colitis (UC) have chronic inflammation of their digestive tracts. While there is no cure for IBD, there are many forms of treatment aimed at reducing symptoms and helping the patient to enter and stay in remission. One form of treatment is with antibiotics.

What are antibiotics?

Antibiotics are medicines used to fight bacterial infections by either killing bacteria, or stopping the bacteria from reproducing (they do not fight viral infections and can potentially worsen a virus).1,2 Some antibiotics used to treat IBD also have anti-inflammatory effects.

While there are many different kinds of antibiotics, the two most commonly used to treat IBD are:2,3

  • Metronidazole (brand name Flagyl)
  • Ciprofloxacin (brand name Cipro)

Another antibiotic that can be used to treat IBD is rifaximin (brand name Xifaxan).3

How can antibiotics help patients with inflammatory bowel disease?

Antibiotics can play two different roles in the treatment of IBD. They can be used as short-term therapy to treat complications of IBD, such as abscesses or wound infections. They can also be used as longer-term therapy for people with IBD, particularly people with CD who have fistulas. Antibiotics are more commonly used in people with CD than people with UC, although they are used in people with UC who experience toxic megacolon.2-4

Even though there is no direct link between specific bacterial infections and IBD, some scientists believe antibiotics can help to reduce IBD-related symptoms by affecting a person’s intestinal bacteria and the intestine’s immune system. Researchers think that antibiotics may help in several different ways:2,4

  • By decreasing the amounts of bacteria and fungus in the gut
  • By changing the balance of microbes in a person’s intestines toward more helpful bacteria
  • By preventing bacteria from invading intestinal tissues and treating tiny, microscopic abscesses there

For some people with IBD, antibiotics are very effective and can be safely used as maintenance therapy if no negative side effects occur.

What are the possible side effects of antibiotics?

Common side effects of taking antibiotics include:2

  • Nausea
  • Headache
  • Vomiting
  • Diarrhea
  • Abdominal pain
  • Yeast infections (thrush or vaginal)

This is not a complete list of side effects. Before taking antibiotics, patients should be sure to read the entire label and follow the directions carefully. It is important not to stop treatment of antibiotics without a healthcare provider’s advice, because stopping treatment too soon may cause a patient to become re-infected by any remaining bacteria.

Some forms of antibiotics affect the breakdown of alcohol and can cause nausea and vomiting. Healthcare providers can provide advice about whether or not to drink alcohol while taking antibiotics. They can also make patients more sensitive to the sun’s UV rays, so it is best to use sunscreen and avoid tanning booths while taking certain antibiotics. Pregnant women or women who wish to become pregnant should also speak with their healthcare providers before beginning an antibiotic treatment regimen.

Patients should make sure to speak with their healthcare provider about possible interactions between antibiotics and any other medications they are taking. For example, birth control pills (oral contraceptives) can be less effective in preventing pregnancy if the woman is taking an antibiotic at the same time. Taking antibiotics at the same time as blood thinning medications can also be very dangerous.

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