What are gut bacteria?
Your digestive tract is home to trillions of tiny living organisms, including bacteria, fungi, and viruses. Together, they are called the gut microbiome.
Many of these microbes help keep you healthy by:
- Helping food digest.
- Supporting your immune system.
- Helping your body work the way it should.
- Making helpful substances, such as short-chain fatty acids from fiber that nourish the lining of your gut.
How do antibiotics affect your gut?
Antibiotics fight bacterial infections. They kill harmful bacteria or stop them from growing.
Sometimes antibiotics also affect the helpful bacteria in your gut.
When you take antibiotics:
- They help treat your infection.
- They may lower the number and variety of the bacteria in your gut for a short time. This is called dysbiosis.
- Most people’s gut bacteria recover over time. Partial recovery usually happens within a few weeks, but full recovery can take months, and some changes may last longer. Recovery varies a lot from person to person and depends on which antibiotic was used.
Should I take an antibiotic?
If your health care provider says you need an antibiotic, take it as directed. Antibiotics can prevent serious illness and complications.
The benefits of treating an infection usually outweigh the effects on your gut bacteria.
Do not stop taking an antibiotic or skip doses unless your provider tells you to. Skipping doses or stopping early can allow the infection to return and help bacteria become resistant to antibiotics.
Why not take antibiotics "just in case?"
Antibiotics help only when they are needed. Antibiotics do not work against viruses, so they will not help with colds, the flu, or most sore throats and sinus infections. Taking antibiotics when you do not need them can:
- Change healthy bacteria in your gut.
- Cause side effects.
- Make some infections harder to treat later because bacteria can become resistant (antibiotic resistance).
This does not mean you should avoid antibiotics. It means you should use them only when your provider recommends them.
Healthy gut tip
Take antibiotics exactly as prescribed. If side effects worry you, call your health care provider before stopping the medicine.
Can antibiotics upset my stomach?
Some people have stomach or bowel changes while taking antibiotics. This is very common — loose stools or diarrhea occur in about 1 in 5 people taking antibiotics.
You may notice:
- Diarrhea.
- More bowel movements.
- Upset stomach.
- Belly pain or cramps.
These problems are usually temporary. Most people get better without long-term issues.
Call your healthcare provider if diarrhea is severe or watery, is bloody, comes with a fever, or lasts more than a day or two, especially after you finish your antibiotics, because this can be a sign of C. diff infection.
What is C. diff?
C. diff (Clostridioides difficile) is a type of bacteria that can sometimes grow after healthy gut bacteria have been reduced.
It can cause diarrhea and other digestive problems, and in some cases, a serious infection of the colon.
Most people who take antibiotics do not get a C. diff infection. The risk is higher in older adults, in people who have been in the hospital, and with certain antibiotics. The risk can stay increased for about 3 months after finishing antibiotics.
How can I help my gut recover?
Fiber feeds the healthy bacteria in your gut. A diet rich in fruits, vegetables, nuts, seeds, legumes (beans/peas/lentils), and whole grains that provide both soluble and insoluble fiber is the approach recommended by gastroenterology experts to help restore healthy gut bacteria.
Regular activity helps your digestive system work well. It can also help keep your bowel movements regular.
Water helps food move through your digestive system. It also helps keep bowel movements regular.
If you have diarrhea, drinking enough fluids also helps you avoid dehydration.
Scientists are still learning how probiotics affect gut health.
Probiotics may help some people, but they are not a quick fix for restoring healthy gut bacteria.
Some studies suggest that certain probiotics may lower the risk of antibiotic-associated diarrhea, but the evidence is not certain, and experts disagree. A recent AGA expert review advises against using probiotics specifically to prevent a C. diff infection. Because guidance differs, whether a probiotic is right for you is best decided with your healthcare provider.
Learn more about probiotics and AGA’s official recommendations.
Questions to ask your health care provider
Ask questions such as:
- Why do I need this medicine?
- What infection is it treating?
- How long should I take it?
- What side effects should I watch for?
- When should I call the office?
- What can I do to support my gut health during treatment?
Remember
Antibiotics save lives. When you need them, take them as directed.
You can support your gut health by eating fiber-rich foods, drinking water, staying active, and following your provider's advice.
Content adapted from an interview with:
Purna Kashyap, M.B.B.S.
Chair of the AGA Center for Gut Microbiome Research & Education Scientific Advisory Board
Reviewed by:
Jessica D. Korman, MD
Capital Digestive Care, Washington, DC
AGA Patient Education Advisor
September 2026