Are Antibiotics Messing With Your Gut?  

3 min read  |  July 02, 2024  | 

Antibiotics are something of a modern science miracle, medications that can treat everything from a urinary tract infection to bacterial pneumonia. However, they can also do a number on your gut.

“Antibiotics don’t discriminate,” says Luis C. Garces, MS, RDN/LD, a dietitian at the University of Miami Health System. “Typically, they get rid of both the bad bacteria and the good bacteria, and that affects your gut microbiome.”

That means a prescribed round of lifesaving antibiotics can kill the bacteria that keep your gut healthy. In fact, some of the side effects — diarrhea, nausea and vomiting, stomach cramping, yeast infections — are directly related to that indiscriminate bacteria killing. However, there are ways to minimize the collateral damage.

But first, a few words about the microbes that live in your stomach and also in your large and small intestines.  Experts say there are about 1 trillion microbes — not only bacteria but also fungi and yeast — homesteading in our body, most of them in our gut.

You can maintain a healthy microbiome through a healthy lifestyle, including by:

  • eating a variety of fruits and vegetables
  • adding fiber to our diet
  • maintaining a regular eating schedule
  • limiting stress

A healthy gut is so important that dietitians and other GI specialists refer to it as our “second brain.”   Research has shown that our gut does more than digest the food we eat. It also signals other parts of our body, such as our brain, liver and lungs.  What’s more, the intestinal tract accounts for about 80% of our immune-producing cells.

When antibiotics unsettle the balance of microbiomes, it’s essential to do everything possible to restore your health by tweaking your diet. But one-size-fits-all doesn’t always.  “That can be a little tricky,” dietitian Garces says. “Not everyone has the same reaction to the same antibiotic.”

That said, Garces has several suggestions to minimize that antibiotic-induced upset stomach feeling:

  • Scale up your consumption of fermented foods. These include yogurt, kimchi, sauerkraut, kefir and kombucha. Garces prefers non-fat Greek yogurt, but any yogurt will do. Just watch for the added sugar.
  • Don’t forget prebiotics, such as leafy vegetables, grains (oats, barley, and whole wheat), onions and garlic, and soybean. Prebiotics stimulate growth and activity of your good gut microbiomes.

However, Garces says that loading up on prebiotics may not always be the right thing to do.

“Those who have diarrhea or are suffering from nausea should actually follow a low-fiber diet during the time period they’re taking antibiotics or experiencing GI issues,” he adds.

  • Consider taking an over-the-counter probiotic supplement. He recommends looking for those that list in their ingredient panel the probiotic strains Lactobacillus rhamnosus GG (LGG) and Saccharomyces boulardii (Sb), which help prevent antibiotic-associated diarrhea. Many over-the-counter supplements contain this, so it is easily accessible. He has also seen physicians suggest Florastor, a popular OTC supplement that restores the natural flora.
  • Do not eat grapefruit. It can reduce the effectiveness of the antibiotic.
  • Avoid taking calcium supplements or eating calcium-fortified foods while taking certain antibiotics. Calcium can interfere with the absorption of tetracyclines and antibiotics known as quinolones (ciprofloxacin, delafloxacin, levofloxacin, moxifloxacin and gemifloxacin.)
  • Drink plenty of water. It keeps you hydrated and flushes out the byproducts of the infection.  It also helps in the absorption of antibiotics.

Headshot of Ana Veciana, author (2023)

Ana Veciana-Suarez is a regular contributor to the University of Miami Health System. She is a renowned journalist and author who has worked at The Miami Herald, The Miami News, and The Palm Beach Post. Visit her website at or follow @AnaVeciana on Twitter.

Tags: gut health, Luis Garces, medicines and your stomach, nutrition care in Miami

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