What to know about replenishing good bacteria after antibiotics

Antibiotics serve an important purpose by killing harmful bacteria that cause infection and illness. However, the activity of antibiotics can also kill the bacteria in your body that is good for you. In particular, it can disrupt the balance of healthy bacteria in your digestive system.

This bacteria, also called the gut microbiome, is critical to many aspects of overall health. You can take steps to put your gut microbiome back into balance after an antibiotic course.

This can include eating certain foods and taking probiotic supplements. Implementing lifestyle measures can also help, such as following a diet that supports the well-being of good bacteria in your gut. 

Key ways you can replenish good bacteria after antibiotics include:

Eating prebiotic foods

Prebiotic foods don’t contain healthy bacteria, but they support their development. These are foods your body can’t digest, but the microbiota in your gut can. Prebiotics, therefore, feed the body’s healthy gut organisms. 

Types of prebiotics include fructooligosaccharides (FOS), isomalto-oligosaccharides (IMO), and xylooligosaccharides (XOS).

Foods that contain prebiotics include:

• onions
• asparagus
• artichoke
• oat
• wheat
• garlic
• chicory

Prebiotic foods also include potatoes and beans. These foods contain resistant starches that can also feed the healthy bacteria in your digestive system.

Eating probiotic foods

Probiotic foods contain live microorganisms that can help populate your gut with healthy bacteria. The National Institutes of Health (NIH) cautions that foods made with live microorganisms might die during processing or during their journey to your gut. Therefore, they might not offer the same health benefits as foods with live microorganisms. 

The NIH says live microorganisms in fermented foods like pickles, sourdough bread, and some yogurts might not survive long enough to offer health benefits. However, microorganisms in yogurts that contain probiotic strains do survive. 

There are many other foods that might contain live microorganisms, but their health benefits remain unclear. Sources of live microorganisms with uncertain benefits include fermented foods like:

• kimchi
• kombucha
• sauerkraut
• miso
• raw unfiltered apple cider vinegar
• kefir

A 2019 paper found that despite their popularity, there’s been little research on the effect of fermented foods on human digestive health. The one exception is kefir, which might have some benefit in getting rid of bad bacteria and for people who cannot digest lactose.

Taking probiotic supplements

In addition to eating prebiotic and probiotic foods, over-the-counter probiotic supplements can also help restore balance to your gut bacteria. It’s important to speak with a healthcare professional first before taking supplements alongside prescription medication. They can identify any possible drug interactions.

A 2022 review of studies suggests taking probiotics while on antibiotics can help prevent damage to your gut microbiome. 

The NIH lists 7 classes of microbial organisms that often appear in commercial probiotics:

• lactobacillus
• bifidobacterium
• saccharomyces
• streptococcus
• enterococcus
• escherichia
• bacillus

Since cultures must be alive at the time of consumption to have health benefits, the NIH recommends reading the label to find the number of colony-forming units (CFUs) alive at the end of the product’s shelf life.

This figure, and not how many were in the package at the time of manufacture, is the most relevant when choosing a product. Most probiotic supplements tend to range from 1–10 billion CFU per dose.

How to maintain a healthy gut microbiome

You can take steps to keep your gut microbiome healthy after a course of antibiotics. As research is limited in this area, there is no specific diet to follow, but some food choices can help support your gut.

Specifically, you can increase your consumption of fermentable fibers and plant polyphenols. Plant polyphenols are antioxidants that have been linked to the prevention of conditions like cancer and cardiovascular disease, as well as inflammatory or neurodegenerative conditions.

Among the foods that may be most beneficial for your gut microbiome are whole plant foods, such as fruits, vegetables, and whole grain cereals.

Which antibiotics can affect your gut health the most? 

The antibiotics that have been most studied for their effect on gut health are broad-spectrum antibiotics. They include these common bacteria-fighting medications:

• amoxicillin (Amoxil)
• ampicillin (Amcill)
• azithromycin (Zithromax)
• erythromycin (Erythrocin)
• metronidazole (Flagyl)
• clindamycin (Cleocin)

If you are taking any antibiotics, consider speaking with a healthcare professional, such as a pharmacist, about whether your medication can affect your gut health.

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Summary

Antibiotics are important first-line treatments that can fight off illness and disease caused by bacteria. Their activity, however, can also kill the good bacteria in your gut.

You can restore these good bacteria by consuming live cultures through food or probiotic supplements. You can support your gut microbiome on an ongoing basis by eating whole foods like fruits, vegetables, and whole grain cereals. 

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