Gut Health While On Antibiotics

Illustration of happy bacteria
Probiotic Illustration by Luke Maxwell

Recently, my daughter and I started a course on antibiotics for two completely different bacterial infections. I was worried because we both have digestive issues and I know antibiotics can be hard on that system. Talking to people, reading my books, and searching the net proved me correct, and gave me information to keep our gut healthy during and after medication.

The Problem with Antibiotics

Yes, antibiotics can cause stomach pain, nausea, diarrhea, and exacerbate existing intestinal problems. Why? Because antibiotics kill bacteria, but they don’t stop with just the infection plaguing you, they wipe out the beneficial microbes in other parts of your body as well.

Our gut is filled with an effective and diverse population of microorganisms (also called “flora”) that help us digest our food to get the nutrients we need. You can put all the healthy food in your mouth you want, but unless your body is breaking it down and absorbing the vitamins and minerals, you will become ill and eventually die. Killing off our natural digestive ecosystem with antibiotics is a dangerous side effect, especially for those prone to stomach upset.

Also, certain antibiotics target specific bacteria. According to my friend Diedre Knauth RN, “This gives other bacteria the opportunity to take over their territory and cause illness. For example, C. difficile is a bacteria many people have and it doesn’t cause a problem. But when someone is on long term antibiotics, C. diff’s competition is killed off, which can cause a terrible intestinal infection and kill your intestines (literally).”

Fighting Back with Probiotics

The key to gut health during and after a course of antibiotics is probiotics, which are active cultures of beneficial bacteria. They can repopulate your intestinal track. One way to get them into your system is to take a probiotic supplement. Be sure to check the label for its intended purpose and make sure that the front label matches the ingredient list on the back. Also, check the expiration date, and look to see if it should be kept refrigerated even before being opened. But since there are no strict regulations, there is an equally effective and yummier way to keep your gut healthy; probiotics in food!

Food Sources of Probiotics

Probiotics that are found in fermented foods go right to your intestines to repopulate your beneficial flora. Fermentation is an anaerobic (without oxygen) cellular process where sugars are converted into acids, gas, or alcohol. Since early human days, fermentation was a way to preserve food and make it easier to digest. It is still a tasty and healthy way to eat. Researchers are finding how important these foods are to overall health. There is an excellent chapter explaining the science behind fermentation in Culinary Reactions: The Everyday Chemistry of Cooking.

Be aware; if fermented foods have been heated up or dried out they are no longer alive, and do not contain the active probiotic cultures. Sourdough bread and dark teas (like Pu-erh) are fermented, and very healthy, but have no living bacteria to repopulate your intestines. If any product has been pasteurized, it no longer contains active cultures. For all the suggestions listed below, be sure to check the label! It should say “contains live cultures” or something similar.

Yogurt is an easy one to find. For example, Brown Cow has four “live” cultures listed on its ingredients list. Kefir generally has more strands of the beneficial bacteria. The flavor tingles your taste buds. You can find kefir by the yogurt section. Cowbella is my favorite local brand.

Fermented vegetables are part of most global cuisines, except the American diet (go figure.) Sauerkraut is from cabbage and most of us know it as a hot dog topping. Fermented pickles and olives are also the traditional way of preserving, but sadly, most brands on the shelf use a quick method that does not have any probiotics in it. Again, check the label. If it doesn’t say, “contains active cultures” assume it doesn’t.

Making your own Fermented Foods

Miso soup base is fermented soy based paste. I bought some paste recently and made an easy, delicious miso soup in my slow-cooker. It should never come to a boil, and therefore continues to keep the cultures alive. Only use the soy paste, not a powder. Kimchi is Korean, spicy fermented cabbage. Pak Dong is the Thai version of fermented vegetables.

Wild Fermentation: The Flavor, Nutrition, and Craft of Live-Culture Foods is a great resource for making your own fermented foods and beverages. I made my first batch of kimchi using the author’s recipe and it was delectable. It’s so easy to make lacto-fermented soda; a sweet, non-alcoholic way to get probiotics in your kids’ system if they are on antibiotics and not thrilled about eating fizzy cabbage…

Other Tips:

According to Tieraona Low Dog, M.D’s book Healthy at Home, “Take your probiotic two hours after each antibiotic dose and continue taking them for four to eight weeks after finishing treatment to encourage the growth of healthy bacteria.”

Aloe vera juice can be very healing, especially if antibiotics cause indigestion. Cut down on refined sugar (this includes white flour.) Bacteria looove sugar and the bad-infection bacteria don’t need any more encouragement. New research shows that diets high in refined sugars and low on fiber can make your intestines porous- a vey bad thing. Your nice gut bacteria will get everything they need from a healthy diet full of prebiotics. Prebiotics are foods that feed your beneficial flora such as leeks, asparagus, chicory, Jerusalem artichokes, garlic, onions, oats, and soybeans.

Happy Ending

I finished my short course of antibiotics, while my daughter is on long-term care, and I’m happy to report neither of us have had stomach problems. Even if you don’t have pre-existing gut issues, adding probiotics to your diet while on antibiotics will help you stay healthy. And keeping them in your diet afterward will ensure you have repopulated with the beneficial flora we all need.

Online Resources

Fermented food research

NIH on probiotics

Intestinal flora

Antibiotic gut problems


Sugar and intestinal problems

Dark Tea information:

Olives as probiotics