Antibiotics may not only harm healthy gut bacteria but also have short- and long-term effects on a person’s health. For example, they can reduce gut flora diversity and affect digestion.

Sometimes, antibiotics are necessary to treat a bacterial infection. However, in the process of killing harmful bacteria, antibiotics can also damage the beneficial bacteria that live in the gut.

Researchers are still learning about the implications of this.

This article explores whether antibiotics harm gut bacteria, which types are most harmful, how they affect health, and how to protect the microbiome while using them.

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Yes, antibiotics can harm a person’s gut flora, including the “good” species that benefit human health.

The gut contains many species of bacteria, viruses, fungi, and other microbes. Scientists associate a high diversity of species with a healthy microbiome. Low diversity has associations with a number of health conditions.

A 2020 review of previous research notes that antibiotic use reduces overall gut flora diversity and disrupts the balance between species.

Review authors link low microbial variety with intestinal inflammation and disrupted intestinal barrier functioning.

Research on how quickly antibiotics affect the microbiome, and how permanent the effects are, varies significantly.

A 2017 review says that even a short course of antibiotics may disrupt the gut microbiome for up to 1 year or more afterward.

However, a 2020 review cites research in which microbial diversity recovered after 6 months.

The 2020 review also notes that age is a factor. It asserts antibiotics during the first 18 months of life cause the most disruption.

The effects of antibiotics on gut health may depend on:

  • the type of antibiotic
  • length of antibiotic course
  • how many previous courses a person has had
  • the person’s gut health before they began taking the antibiotics

Repeated antibiotic treatment may prevent a full recovery from ever occurring.

A 2015 study explored the effects of four common antibiotics across fecal and saliva samples. The antibiotics were:

Clindamycin significantly reduced fecal microbiome diversity for up to 4 months. Ciprofloxacin reduced fecal microbiome diversity for up to 12 months.

There was only a short-term reduction in the saliva samples immediately after exposure to ciprofloxacin.

Researchers found a significant reduction in microbiome diversity in fecal and saliva samples directly after exposure to minocycline.

Amoxicillin had no significant effect on microbiome diversity in either sample.

Further research from 2015 also found that exposure to ciprofloxacin or clindamycin significantly affected gut flora diversity. Researchers observed changes for up to 1 year.

There are many types of antibiotics, though, so this is not a comprehensive list. People may need to research the specific type they are taking or ask their doctor to understand the risks.

Antibiotic-related gut bacteria changes can have negative implications for a person’s health, including:

Antibiotic resistance

Antibiotic treatments can lead to antibiotic resistance.

Researchers define antibiotic resistance as a bacterium’s ability to elude the effects of certain antibiotics that usually inhibit or eradicate other bacteria from the same species.

The World Health Organization (WHO) states that there is an antimicrobial resistance crisis. The WHO estimates that antibiotic resistance-related deaths could reach 10 million by 2050.

Clostridioides difficile

Clostridioides difficile (C. diff) is a harmful type of bacteria that lives in the intestines.

Usually, other microbes can keep C. diff under control, but antibiotics can allow the bacterium to grow. This can lead to antibiotic-associated diarrhea, which can pose a serious risk to a person’s life.

Digestive health

Antibiotics may affect digestion. The 2020 review mentioned above states that observational studies have implicated antibiotic use in increasingly occurring conditions, such as:

A 2010 study with Danish children reported that the likelihood of developing IBD was highest in the first 3 months after taking antibiotics. The risk was highest in children who had received at least seven courses of antibiotics.

Metabolic conditions

The 2020 review also found evidence that low microbial variety correlates with an increased risk of developing metabolic diseases, including:

Changes to the immune system

The microbiome influences the immune system, both of which develop at the same time during infancy. Disruption of the microbiome, particularly in childhood, may then affect how well the immune system functions.

Previous studies in mice have found that antibiotics can affect how the immune system matures. They can reduce the thickness of mucus in the colon and the development of the intestinal lining. Both of these effects can raise the risk of infection.

Further research in humans is necessary.

Allergic conditions

A 2022 review found evidence of links between antibiotic administration in early life and a heightened risk of allergic conditions, such as:

There are practical steps people can take to protect their gut health when taking antibiotics.


A 2022 review notes that several studies have found probiotics can partially restore gut flora after taking them. Certain types of probiotics may help stabilize the microbiome during treatment or prevent harmful microbes from taking over.

However, the type and dose of probiotics are important.

A 2021 study found that a combination of Lactobacillus rhamnosus and Saccharomyces boulardii were effective, but more research is necessary to validate this.

Probiotics are not without risks. People should ask a doctor about the pros and cons before taking them.


Prebiotics are substances that feed bacteria. A 2015 study found that a high fiber diet and prebiotics can help stimulate the growth of Bifidobacterium. Prebiotics also restored metabolic function and microbiota composition.

Learn more about what to eat when taking antibiotics.

The best way to avoid the negative effects of antibiotics is to minimize exposure to them. This means doing the following:

Avoid unnecessary antibiotic use

Antibiotics only treat bacterial infections. They will not help viral illnesses, such as:

  • colds
  • flu
  • COVID-19

Even when a person does have a minor bacterial infection, antibiotics may not be necessary. For example, sinus infections and ear infections can often clear up on their own.

Prevent infections

Preventing bacterial infections can reduce the need for antibiotics. The same is also true for viral illnesses.

Although they are not bacterial to begin with, bacterial infections can start as a complication of colds and flu.

To prevent contracting and transmitting these illnesses:

  • Wash hands with soap and water for at least 20 seconds after using the bathroom and before preparing or touching food.
  • Use hand sanitizer that contains at least 60% alcohol when handwashing is not possible.
  • Cover the mouth and nose with tissue when coughing or sneezing.
  • Stay home when sick.

Other conditions that can ultimately require antibiotics include some sexually transmitted infections (STIs), some types of food poisoning, and others that have their own prevention methods.

Use antibiotics only when necessary

Sometimes, antibiotics are necessary, even when a person tries to avoid them. People may need antibiotics for an infection that is spreading or getting worse, or for life threatening conditions, such as pneumonia and sepsis.

Doctors may also prescribe antibiotics for people who have a high risk of developing serious infections, including:

According to the Centers for Disease Control and Prevention (CDC), the benefits of antibiotics usually outweigh the risks for people who require them.

However, each individual should speak with a doctor to determine the best course of action.

Antibiotics can harm healthy gut bacteria because they do not discriminate between the “good” and “bad” species.

Antibiotics have links to antibiotic resistance, reduced microbial diversity, allergies and eczema, metabolic conditions, and digestive conditions, such as IBD. The changes in gut flora composition can be short term but can also be long term.

When antibiotics are necessary, taking probiotics, such as S. boulardii, may reduce their effects on gut bacteria. A balanced, high fiber diet that contains prebiotics may also help.

People concerned about antibiotic use can speak with a doctor about the benefits and risks.