The unfortunate side effect of antibiotics is its negative impact on gut health.

Antibiotics have the ability to halt infectious diseases that were once debilitating or deadly. However, one of the unfortunate side effects is its negative impact on gut health.  Learn how it can be recovered through the right foods and diet.


Antibiotics are commonly used to kill infectious bacteria or to prevent an infection from occurring, such as after a surgery. What many do not realize, and what many doctors do not mention, is that antibiotics can do quite a bit of harm too.

Antibiotics, which are largely overprescribed, are non-selective, meaning they kill the “bad” bacteria as well as the “good” bacteria that live in the gut.

The “good” bacteria, your gut microbiota, are made up by over 1,000 different species and subspecies of bacteria that live in your intestines. They are a diverse community of bacteria helps you to break down food, synthesize various nutrients, keep harmful substances from entering your body, and strengthens your immune system.

When the community is disrupted, it can quickly become unbalanced and creates a greater risk for disease and inflammation.

By killing the good guys, antibiotics undo the balanced relationship that exists between you and your gut bacteria. As a result, the diversity and quantity of bacteria strains decreases.

When important members of the bacterial community are killed off, those that remain have a difficult time carrying out all of the important functions because they don’t have the support from the rest of the community.

Resistant members of the community, meaning bad bacteria that are extra strong, are able to survive in the face of an antibiotic. Increases in these resistant members makes you more prone to further infection and development of antibiotic resistant disease.

Doesn’t sound good? It isn’t.

The extent of the changes to your gut microbiota will depend on the strength of the antibiotic and the length of time it is taken. However, regardless of type and time there are things you can do to protect yourself and your gut community:


Make sure to select a good quality, pharmacy grade probiotic. When it comes to probiotics, buying one at the grocery store may be cheaper, but those are not always best. The antibiotics have wiped out your good gut bacteria so you want a probiotic with a variety of strains since you want to replenish as much of the bacteria as you can.

Look for a high CFU (colony forming units) count, which are the amount of live cells capable of forming new colonies. Generally, looking for 25-50 billion CFUs and the greatest number of strains will be the most helpful.


Glutamine is an amino acid that improves gut function, intestinal development, and immunity. It repairs and replenishes the cells that line your intestines, thereby keeping your intestinal barrier strong and keeping harmful things from being absorbed.

Although we can get glutamine from our food, after a period of stress, disease, or infection, extra glutamine support in the form of L-glutamine may enhance your gut repair and help it stay balanced.


Fermented foods naturally contain probiotics! A probiotic supplement will help replenish your gut bacteria, but the more sources and variety you can get the better! Fermented foods include kefir, sauerkraut, kimchi, and kombucha. You can also try Kevita, a slightly carbonated drink with probiotics added.

Yogurt is the most popular way that probiotics are consumed through food, although some brands may not contain a high quantity or variety of active probiotics as the above mentioned fermented foods. Try Greek yogurt, which is more concentrated in probiotics than regular yogurt.

Here’s a fun fact: did you know that kefir, a drinkable yogurt, is the highest naturally containing probiotic food? Get the plain, unsweetened version, blend it with fruit to make a smoothie, or drink a glass before bed.


Diet has a major effect on your gut microbiota. The typical American diet, also known as the Standard American Diet (SAD) or a “Western” diet, is high in omega-6 fats, low in omega-3 fats, high in processed foods and added sugar.

In one research study, switching mice to a diet that mirrored the SAD diet, rich in sugar and Omega-6 fats, showed changes in the microbiome in just one day. At two weeks the mice showed increased fat tissue.

A SAD diet has also shown to have a negative impact on many strains of gut bacteria. When your gut health is already taking a hit from the antibiotics, do not aggravate it by adding a poor diet into the mix. Avoid a SAD diet and eat real food.

For more information, read the full article.

Courtney Ferreira, MS, RD, LDN is a Registered Dietitian based in Baltimore, MD with a passion for helping individuals reach their health and wellness through flavorful whole foods and freedom from counting calories, fat, and minutes on a treadmill. For more insightful tips on living your healthiest life from Courtney, visit her at the RealFoodCourt.

  1. I really need some help.2 years ago I had cdiff. I was on four different antibiotics because it wouldn’t go away. My stomach is royally out of wack even after 2 years…. Please any help would be appreciated

  2. I have had multiple surgeries, about 20 doses of antibiotics and zero good bacteria. How can I heal my gut with Crohns disease.