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Taking an Antibiotic? Here’s What You Need to Know

antibiotic digestion fertility gut health guthealth Jan 16, 2023

Antibiotics are very important. Antibiotics are potent, life-saving medications that allow serious, potentially fatal infections to be treated. However, there is a growing problem: antibiotic overuse. And, as with most things, going too far can have unintended consequences.

That’s why in today’s blog post, I'm going to discuss what antibiotics are, antibiotic overuse, potential side effects, and how it can affect your gut microbiome. Let’s get into it…


What are antibiotics? 

Antibiotics are medications that are used to treat bacterial infections in humans and animals by either killing the bacteria or making it difficult for the bacteria to grow and multiply.

Antibiotics, on the other hand, do not cure everything, and overuse of antibiotics can be harmful.

Antibiotics can be used to treat the following infections:[1]

  • Some ear and sinus infections
  • Dental infections
  • Skin infections
  • Meningitis (swelling of the brain and spinal cord)
  • Strep throat
  • Bladder and kidney infections
  • Bacterial pneumonias
  • Whooping cough
  • Clostridium difficile

Only bacterial infections can be killed with antibiotics. Viruses are responsible for the majority of sore throats, the stomach flu, the common cold, the flu, most coughs, some bronchitis infections, and the common cold, which cannot be cured by antibiotics.[1] In order to treat these infections, your doctor will either advise you to wait them out or will give you antiviral medications.

Image by University of Waterloo


Antibiotic overuse

According to data published in the Journal of the American Medical Association (JAMA) by the CDC, 1 in 3 antibiotic prescriptions are unnecessary.[2] 

The study examined the usage of antibiotics in emergency rooms and medical offices across the country. According to CDC researchers, the majority of these unnecessary antibiotics are prescribed for viral respiratory illnesses, such as sinus and ear infections, bronchitis, viral sore throats, and common colds, which do not react to antibiotics.[3] Patients who receive these 47 million extra prescriptions per year run the unnecessary risk of developing allergic reactions or Clostridium difficile (which cause diarrhea that can lead to severe colon damage and sometimes even death).[2] 

What’s more is that antibiotic resistance can develop as a result of antibiotic misuse. This happens when bacteria change and resist the effects of an antibiotic. In other words, resistant bacteria may continue to grow and multiply even though someone is taking antibiotics. The threat of antibiotic resistance is that infections (such as pneumonia, strep throat or infections associated with minor injuries) could become untreatable.[3]

Examples of antibiotic misuse include:[3]

  • giving antibiotics to people and animals when they are not needed,
  • taking antibiotics in ways other than how they were prescribed,
  • self-medicating or antibiotic sharing,
  • taking antibiotics for an infection that is not caused by a bacteria.  

What are the side effects if using antibiotics? 

Many of my gut health clients report having used quite a few antibiotics in their lifetime. It could have been for chronic urinary tract infections, sinus infections, surgeries, a tooth infection, etc. Many report their digestive issues getting progressively worse afterwards. Antibiotics can have several negative impacts on host health; both direct and indirect effects. The gut microbiota plays a crucial role in host health regulation. Effects of antibiotics on the host through the gut microbiome are immense and can affect various functions including immune regulation, metabolic activities, and thus overall health [4]. 

The side effects of antibiotics range from minor to very severe. Some of the common side effects include:[5]

  • Rash
  • Nausea
  • Diarrhea
  • Yeast infections 

More serious side effects can include:[5]

  • C. diff infections
  • Severe and life-threatening allergic reactions
  • Antibiotic resistance infections

A 2017 study, published in JAMA Internal Medicine, that examined nearly 1,500 adult patients admitted to Johns Hopkins Hospital found that 1 in 5 patients suffers antibiotic side effects.[6] The most common side effects were abnormalities with the gastrointestinal system (42%), kidney (24%), and blood (15%).[6]

Additionally, for up to 90 days, researchers monitored patients for the development of new multidrug-resistant infections as well as for the bacterial infection, Clostridium difficile, which can cause severe diarrhea.[6] In total, 4%of patients developed the first infection (Clostridium difficile), and 6% developed a multidrug-resistant infection.[5] Notably, researchers came to the conclusion that 19 percent of the antibiotics given to patients were unnecessary clinically to begin with.[7]


How can antibiotics impact your gut microbiome?

Treatment with antibiotics frequently alters the intestinal microbiome and, by reducing microbial diversity, can result in a loss of microbial metabolism (causing osmotic diarrhea from too much fluid in the intestine), a loss of colonization resistance (resulting in an increase in infections from other pathogens), and an increase in intestinal motility.[8]

The change in gut microbiota caused by antibiotics can cause diarrhea, also known as antibiotic-associated diarrhea. In fact, it’s estimated that up to 30% of people taking antibiotics can have diarrhea caused by taking the antibiotic.[8]

According to a 2020 review, depending on the type and dosage of antibiotics, our gut microbiota often returns to (near) normal within a few weeks.[8] A 2015 study, however, found that our gut microbiota can "bounce back" after antibiotics for up to 12 months, and in some people, even after 12 months, their gut microbiota still hadn't entirely recovered. This is why it's important to exercise caution and make an informed decision before taking antibiotics.[8]


Here’s what you or someone you know can do if you have to take an antibiotic:

  1. Eat prebiotic foods and aim for 30+ different plant foods per week. Simply put, prebiotics are a source of food for your gut’s healthy bacteria. They’re carbs your body can’t digest and they travel to your lower digestive tract where they act as food to encourage the growth of good bacteria! Examples of prebiotic foods include: Apples, bananas (especially green bananas), asparagus, onions, garlic, ground flaxseeds, and oatmeal. You can learn more about prebiotics here
  2. Take a probiotic within the 1st two days of starting antibiotics and continue to take them until a week after you stop the antibiotic. This has been shown to significantly decrease your risk of antibiotic-associated diarrhea.[8Probiotics are live cultures of "good" bacteria similar to those that are naturally present in your stomach. Their main job is to maintain or improve the "good" bacteria (normal microflora) in your body. You can learn more about probiotics here
  3. Finish antibiotic course to avoid antibiotic-resistance. That’s right, even if you feel better you should still finish the course of your antibiotics! It's possible that the bacteria can remain in your body even after your symptoms disappear and if you stop taking your antibiotics before the antibiotic cycle is finished, the remaining bacteria can continue to multiply.[9] 

 This is a great resource created by Alberta Health Services: Wise Guide to Antibiotics


  1. What are antibiotics? WebMD. Retrieved December 29, 2022.
  2. CDC: 1 in 3 antibiotic prescriptions unnecessary. (2020, October 2). CDC.
  3. About antibiotic resistance. (2016, January 1). Canada.Ca.
  4. Impacts of Antibiotics on the Human Microbiome and Consequences for Host Health
  5. Antibiotics. (1999). Drug Therapy
  6. Study finds 1 in 5 patients suffers antibiotic side effects. (2017, June 16). The Hub.
  7. Retrieved December 29, 2022, from
  8. Rossi, M. (2022, June 1). Antibiotics: your questions answered. The Gut Health Doctor.
  9. Why is finishing antibiotics so important? Retrieved December 29, 2022.

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