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Are Antibiotics Bad For Your Gut?
Updated on February 27, 2023
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Are Antibiotics Bad For Your Gut?

Antibiotics may be bad for your gut.

While they do a great job of killing bad bacteria, they also deplete good bacteria in the human gut. This is bad news for your overall intestinal health.

Beneficial bacteria prevent bad bacteria from overpopulating your intestinal mucosa. Antibiotics can wipe them out, causing an imbalance in your gut flora.

We sat down with Dr. Rizza Mira, a general practitioner, to find out which antibiotics are bad for your gut. More specifically, we wanted to know which types cause diarrhea.

Dr. Mira frequently prescribes antibiotics for her patients, so she's quite familiar with antibiotic drugs and their effects on the human body.

Are Antibiotics Bad For Your Gut? 2

Can Antibiotics Cause Diarrhea?

Yes. Antibiotics can cause diarrhea, although most people tolerate antibiotic treatment with minimal symptoms. But some may experience diarrhea and other digestive symptoms.

About one in five people who take antibiotics have antibiotic-associated diarrhea (AAD). AAD happens when you pass loose and watery stools while taking antibiotics.1 

“Antibiotic-associated diarrhea is having at least three (3) watery stools per day. These symptoms show anywhere from a few hours to 2 months after the intake of antibiotics. It occurs in 5 to 20% of the population,” says Dr. Rizza Mira.

It usually takes a week of treatment before the symptoms appear. The effects of antibiotics can last for days to months after you stop treatment.

In most cases, AAD is mild and clears up within days of stopping drug use. However, some people may have worse symptoms.

You should call a doctor as soon as possible if you have:

  • Severe diarrhea
  • Fever
  • Bloody stool
  • Intense stomach pain

You may need to switch to a different medication or stop taking it.

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Why Do Antibiotics Cause Diarrhea?

Antibiotics kill harmful bacteria and prevent them from spreading infectious diseases. While doing so, they're also destroying beneficial bacteria in your gut.

Your gut microbiome depends on a natural balance between bad and good gut microbes. Antibiotics can disrupt that balance, leading to digestive irritations. They can also reduce gut microbial diversity and cause gut dysbiosis or imbalance.

The decrease in healthy bacteria may lead to harmful bacteria taking over. These bad microbes produce toxins that damage the gut and cause intestinal inflammation and diarrhea. 

Clostridium difficile (C. difficile) is one of them. It produces toxins that may cause severe AAD. About 25% of all AAD is caused by a C. difficile infection.2

Candida (a fungus) may also cause antibiotic-associated diarrhea. Other types of pathogenic bacteria that can take over during AAD are:2

  • Clostridium perfringens
  • Staphylococcus aureus
  • Klebsiella oxytoca
  • Salmonella

People who are over 65, have a weak immune system, or have been hospitalized for long periods have the highest risk for AAD.3

Which Antibiotics Cause Diarrhea?

Most antibiotics cause diarrhea, but some are less likely to cause side effects. For example, narrow-spectrum types target specific harmful bacterial species, so they may not give you diarrhea.

Broad-spectrum antibiotics are more likely to trigger diarrhea. It's because they kill many types of bacteria—both good and bad.

Below are some of the potentially worst antibiotics for gut microbiota.


Penicillins are the very first types of antibiotics discovered. Doctors commonly prescribe them, even to this day.5 

They are mainly used for infections of the upper respiratory tract. However, they can also treat kidney, bladder, and gastrointestinal bacterial infections.

Penicillin blocks the ability of harmful bacteria to make cell walls. If bad bacteria can’t make cell walls, your immune system can easily target them.5 

Ampicillin and amoxicillin are the types of penicillin most likely to cause diarrhea.2 According to Dr. Mira, penicillins combined with clavulanic acid may also worsen diarrhea.


Cephalosporins are commonly prescribed to treat urinary tract infections (UTIs). But they can also treat bacterial infections in different body parts, including:

  • Ear infections
  • Sinus infections
  • Skin infections
  • Respiratory infections

Doctors may give cephalosporins as an alternative treatment for people allergic to penicillin. Cefuroxime and cephalexin are two examples of this drug.


Tetracyclines such as doxycycline and minocycline treat respiratory and skin infections. They can also help with infections spread by ticks and animals.

Even if they cause diarrhea, you can use them to treat traveler’s diarrhea. Traveler’s diarrhea is a travel-related illness where you pass three or more loose and watery stools in a day. People can get it from drinking or eating contaminated food and water while traveling.6


Macrolide antibiotics like erythromycin and clarithromycin treat many acute and chronic infections. But they’re also some of the worst antibiotics for your gut.

Macrolides destroy beneficial bacteria and disturb the human gut microbiota.7

Ways to Restore Your Gut Flora After Taking Antibiotics

Mild cases of diarrhea usually clear up after you stop taking antibiotics. You can help your gut microbiome recover by introducing healthy bacteria or probiotics into your diet. You can also take foods that promote their growth in your gut or prebiotics.

Eat Probiotic and Prebiotic Foods

Probiotic foods contain lots of beneficial gut bacteria. They’re a great way to improve your gut health and repopulate it with good bacteria.

Fermented foods like the following are rich in probiotics:

  • Yogurt 
  • Sauerkraut 
  • Kimchi
  • Kefir
  • Tempeh

On the other hand, prebiotics are fibers that serve as food to your healthy gut bacteria. You can get prebiotics from fiber-rich foods like onions, legumes and fruits like apples and bananas. 

Take Probiotic Supplements

If probiotic foods aren’t your thing, you can try some of the best probiotic supplements. They usually contain more live bacteria than probiotic foods. 

Probiotics also contain specific types of bacteria that are more likely to improve gut health.

“Lactobacillus, Bifidobacterium, and Saccharomyces genus are the best-studied probiotics that seem to benefit people the most, especially children,” says Rizza Mira, M.D.

Studies show that taking certain probiotic supplements during and after antibiotic treatment can reduce your risk of developing AAD.8

When taking probiotics, aim for a supplement that contains at least 1 billion colony-forming units (CFUs). CFU indicates the number of bacteria per serving.

The Takeaway

Antibiotics disturb your gut flora but can treat a harmful bacterial infection. They're used for treating deadly infections, so you should take them responsibly — use them only as prescribed.

Prolonged misuse and overuse of antibiotics may lead to antibiotic resistance. Some bacteria adapted and developed antibiotic resistance due to years of improper antibiotic usage.9

It’s also essential to restore your gut flora after antibiotic treatment. Some doctors prescribe probiotic supplements to prevent recurring diarrhea.

You may also eat prebiotic fiber foods like whole oats, nuts, berries, etc. Your body can’t digest fibers, but your good gut bacteria can. Prebiotic fibers help stimulate their growth.

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Updated on February 27, 2023
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9 sources cited
Updated on February 27, 2023
  1. Antibiotic-associated diarrhea.” Mayo Clinic.
  2. Antibiotic associated diarrhoea: infectious causes” Indian Journal of Medical Microbiology.
  3. Managing antibiotic associated diarrhoea British Medical Journal.
  4. Narrow-spectrum antibacterial agents” MedChemComm.
  5. "Penicillin Allergy." National Center for Biotechnology Information.
  6. "Tetracycline." National Center for Biotechnology Information.
  7. Unravelling the collateral damage of antibiotics on gut bacteria” Nature.
  8. Probiotics for the Prevention of Antibiotic-Associated Diarrhea in Outpatients—A Systematic Review and Meta-Analysis” Antibiotics.
  9. "Antibiotic resistance." NHS UK.
Dr. Rizza Mira
Dr. Rizza Mira
Medical Reviewer
Dr. Rizza Mira is a medical doctor and a general practitioner who specializes in pediatrics, nutrition, dietetics, and public health.

As a pediatrician, she is dedicated to the general health and well-being of children and expecting parents. She believes that good nutrition, a healthy lifestyle, and prevention of illness are key to ensuring the health of children and their families.

When she’s not in the hospital, Rizza advocates and mobilizes causes like breastfeeding, vaccination drives, and initiatives to prevent illness in the community.
Will Hunter
Will Hunter
Content Contributor
Will is a content writer for KnowYourDNA. He received his B.A. in Psychology from the University of California, Los Angeles. Will has 7 years of experience writing health-related content, with an emphasis on nutrition, alternative medicine, and longevity.
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