Let's Personalize Your Experience!

Where would you like to shop? Please click the logo below.

young woman holding stomach

How To Support Your Gut While Taking Antibiotics

Though we know antibiotics impact our gut microbiomes in a major way, sometimes theyre necessary in order to promote healing and prevent health complications. 

For example, according to the Centers for Disease Control and Prevention (CDC), antibiotics are often prescribed when someone is battling a bacterial infection such as pneumonia or Lyme disease. They can also be critical for people at high risk for infections, such as those undergoing surgery, patients with end-stage kidney disease, or those receiving chemotherapy.

Despite their importance in certain circumstances, though, antibiotics can also deplete the “good bacteria” living in the gut while they knock out the harmful types. Plus, when antibiotics are overused and prescribed for conditions they aren’t needed for, germs develop the ability to defeat the very drugs designed to kill them, a growing problem known as antibiotic resistance. 

The good news: During and following a course of antibiotics, there are several steps you can take to get your gut back on track and balance the amounts and types of microbes (including yeast and bacteria) living in your gastrointestinal system.

From how to supplement and what to eat to general lifestyle tips, the following strategies can help you holistically show your gut some much-needed TLC.

Supplement Recommendations

Even in situations in which you choose to use antibiotics to help overcome an infection, you can still boost your gut health and immune defenses with a few specific herbs, nutrients, and other supplements.

Some of the most highly recommended supplements for immune and gut support include:

You can incorporate these helpful supplements into your routine both while you’re taking antibiotics and after you finish up your course for continued support.


First thing’s first: In order to help heal your gut and replenish good, protective bacteria, most experts recommend seeking out a high-quality probiotic supplement to take while on antibiotics. 

Probiotics are the friendly” bacterial flora living inside of the digestive tracts that help us break down food and absorb immune-boosting nutrients. Its well-established that probiotics can help support overall gut health and immune function, at least partially by keeping the growth of harmful bacteria in check. 

Look for probiotic supplements that contain soil-based organisms (SBOs), which are considered “hardy” types of microbes capable of surviving harsh conditions in the body on their way to your gut.

Ideally, aim to consume between 20 and 100 CFUs (colony forming units, a measure of a supplement’s strength or potency) of probiotics daily. You’ll also want your supplement to contain multiple strains, including those in the Lactobacillus and Bifidus family, to support your gut in multiple ways.

Since each product varies a bit, read label directions carefully.

During your course of antibiotics, aim to take probiotics a few hours later and on an empty stomach (like between meals). Once you’ve finished your antibiotics, take your probiotics first thing in the morning to stay consistent.


Another helpful supplement for immune and gut support is garlic. You can reap the benefits by eating garlic raw or by taking a garlic oil or garlic supplement. Garlic contains many immune-supporting compounds (including organosulfur compounds allicin and alliin).

Oregano Oil

Oregano oil makes for another incredible addition to your wellness routine—especially while taking antibiotics. You may love the whole herb for its culinary use, but it also has a long history of bolstering the immune system, thanks to powerful compounds called carvacrol and thymol that it contains. To support your body during and after taking antibiotics, incorporate a serving of an oregano oil supplement twice daily for up to 10 days. 

Vitamin C

Also, consider upping your intake of vitamin C, an essential vitamin that generally supports a healthy immune system. If you choose to supplement, take at least 75 to 90 milligrams of vitamin C (the daily recommended amount for adults) once a day with a meal.

Echinacea and Elderberry

Finally, herbs such as echinacea and elderberry contribute to a healthy intestinal barrier and support the body’s immune response. Often, they come in handy when you’re already feeling under the weather.

Read More: Are You Unconsciously Hurting Your Immune Health?

You can take a serving of an echinacea supplement up to two to four times per day for up to 10 days. (Make sure to read the directions for the specific product you’re taking). You can also incorporate one tablespoon of elderberry extract syrup up to four times a day for 10 days.

Diet Changes

The first priority when battling an illness is to make sure you stay hydrated. This is especially true when taking antibiotics because they can often lead to diarrhea. So, to prevent dehydration and electrolyte imbalances it’s important to drink lots of fluids, focusing on regular water, coconut water, and herbal teas.

Beyond that, incorporating certain foods that offer gut support and help the body fight bacteria can also do your system a solid. A whole slew to include in your diet daily if possible include: 

  • Probiotic foods, such as apple cider vinegar, cultured dairy products like kefir or yogurt, fermented vegetables like sauerkraut and kimchi, and probiotic beverages like kombucha and coconut kefir.
  • Garlic (especially raw garlic)
  • Onions
  • Herbs like oregano, parsley, cilantro, and rosemary
  • Prebiotic foods (which help “feed” probiotics in the gut), including asparagus, raw chicory root, raw Jerusalem artichokes, and dandelion greens
  • Manuka honey
  • Mushrooms
  • Foods high in vitamin C, like leafy greens, citrus fruits, and berries
  • Turmeric and ginger

Try to have one or two servings of probiotic-rich foods per day during and immediately after taking antibiotics—and incorporate as many of these other helpful foods as is reasonable.

Foods To Avoid

In addition to emphasizing these gut- and immunity-nourishing foods, you may also want to consider whether certain foods in your diet are exacerbating symptoms and delaying healing. A few to be critical of: common allergens, sugary foods and drinks, and processed foods. 

When it comes to allergens, the anti-nutrients and proteins like phytate, lectin, and gluten in grains, for example, may be difficult for some people to digest—and you’ll want to avoid putting any unnecessary stress on your gut during and post-antibiotic use. Dairy can also be hard for some to break down properly.

Too much sugar, meanwhile, can tax your gut by potentially exacerbating already-established candida yeast issues. Plus, some people find that sugar increases symptoms like bloating.

Read More: 10 Foods That Pack More Added Sugar Than You Should Have All Day

And, as for processed foods, it’s best to limit refined grains, sweets, and processed meats, which are low in nutrients and poor substitutes for things like vegetables, fruits, and quality proteins. The more room you make in your diet for the helpful foods listed above, the better.

Other Lifestyle Tips

First, get enough rest. Sleep is very important when healing, and for your gut-brain connection. This connection refers to the communication that occurs between the intestines and the brain, which influences hormone production as well as the production of white blood cells (which, yes are mostly made in your gut!). Your task: Aim for at least seven to eight hours of shut-eye per night.

You’ll also do well to get as much fresh air and sunlight as possible (safely, of course). Once you feel well enough, starting to reincorporate movement that feels good (whether it’s yoga or walks) can also lift your energy and mood.

Also, since your immune system is already compromised if you’re sick enough to require antibiotics, keep everything in your home as clean as possible. Wash your hands thoroughly, clean your kitchen and bathroom surfaces well, and cover your mouth and nose when sneezing or coughing.

Finally, make sure to follow antibiotic prescription directions very carefully. Dont skip doses, double up on doses, or stop without finishing the cycle. This helps ensure that the infection you’re dealing with will actually be cleared so that you can fully heal. Otherwise, should harmful bacteria continue to proliferate, you may end up needing another round of antibiotics. 

Dr. Josh Axe, D.N.M., D.C., C.N.S., is a doctor of natural medicine, clinical nutritionist, author, and member of The Vitamin Shoppe’s Wellness Council. Dr. Axe operates one of the world’s largest natural health websites, sharing healthy recipes, herbal remedies, nutrition and fitness advice, and information on essential oils and natural supplements. Dr. Axe founded one of the largest functional medicine clinics in the world, in Nashville, TN, and has served as a physician for many professional athletes.

(Visited 6,232 times, 1 visits today)