Gut Performance Blog

The Effects of Drugs and Gut Bugs

Most people clearly understand that antibiotics can harm your gut health. All you have to do is experience the resulting diarrhoea or abdominal pain during the course of this type of treatment!

Health professionals have been aware of the potential damage of antibiotics for a long time. It’s one of the several reasons doctors are reluctant to prescribe them when they are not specifically required. It is also why integrative doctors prescribe a course of prebiotics and or probiotics to counteract the damage that some antibiotics do. 

But, are you aware that nearly a quarter of non-antibiotic drugs can have a similar effect on your gut health?

But this isn’t the whole story about drugs and our gut bugs. 

Let’s dig a little deeper and find out how our gut bacteria affect the drugs we take and how the medicines we take affect our microbiota.

The Effect of Microbes on Drugs 

The gut microbiota is almost like a pharmacy within our body. They can affect the effectiveness and the toxicity of the drugs we are prescribed. 

Depending on the types of bugs in our gut, they interact with the drugs we consume in two predominant ways. 

  1. Gut bacteria can increase the bioavailability of a drug to the body. It can also decrease the bioavailability of a drug.  
  2. It can increase the toxicity of a drug to the body. 

Both these actions can affect health outcomes for the individual. It’s not all bad….there is an understanding that metformin (a Type 2 Diabetes drug) is improved by bacterial short-chain fatty acid producers in the gut, improving insulin resistance and helping reduce the gastrointestinal effects of this drug (de la Cuesta-Zuluaga, et al., 2017). Notably, there are more adverse consequences documented than beneficial relationships.

The Effect of Drugs on Beneficial Microbes

Fun fact – Of 835 non-antibiotic drugs tested in a recent study on common gut flora in a healthy human gut, 24% (203) had a significant effect on the gut microbiome (Maier, et al., 2018) . 

Most of the 203 drugs only inhibited the growth of a few strains, but 40 of the medications affected at least 10 strains! It should also be noted that the doses used in their study were well within relevant concentrations that a human would be prescribed. 

Drugs influence gut microbial composition differently, but there are two main actions (Weersma, Zhernakova, & Fu, 2020). 

  1. Drugs facilitate the movement of the microbiome from other body sites to the gut, causing dysbiosis. This often happens in reflux, where PPIs are used to reduce stomach acidity. However, this allows harmful oral microbes to pass through the stomach to the gut, where they wouldn’t usually populate.
  2. Drugs change the intestinal environment and directly affect bacterial growth. This mode of action can be bidirectional. This means it can promote the growth of certain bacteria, but drugs can also inhibit the growth of specific bacteria.

Drug Categories that Effect the Gut 

It is no surprise that antibacterials inhibit pathogenic bacteria but also normal bacteria. The same can be said for most antifungals, antivirals, and antiparasitic drugs tested. 

Other categories of drugs that have been found to impact the gut microbiota, include specific cancer therapies, anti-inflammatories, antihistamines, NSAIDs, antipsychotics, antihypertensives, and antiarrhythmics anticoagulants, and hormones/hormonal modulators.

The categories with the most significant impact on the microbiota seem to be proton pump inhibitors (PPI’s), commonly used to treat indigestion and reflux, antibiotics used to treat bacterial infections, and laxatives used to treat and prevent constipation (Maier, et al., 2018). 

Another point to consider is polypharmacy…just ask any nurse, doctor, or pharmacist. They know that very few people take just ONE medication. If a person is taking multiple drugs, the potential damage to gut health quickly increases. 

While pharmaceuticals are valuable in treating disease, the short and long-term effects of medication need to be considered. Side effects come with all drugs, but the actions on the microbiome suggest that treating one disease with medication can potentially cause another disease later. It is time to consider or act on adjunctive treatment to protect gut health when taking medications. 

The Microbes Affected

Microbial responses to drugs varied across all studies; however, overall, it has been found that the bacterial species with the highest abundance in healthy individuals was the one that was significantly susceptible to these drugs (Maier, et al., 2018). 

What are the most important actions to take to protect my gut?

Our diet and medications are major drivers in our gut microbiota composition and diversity. It is essential to fully understand the consequences of what we put in our mouths, including the drugs we take.

Of course, other factors such as diet, lifestyle, sleep cycles, stress, exercise, and the presence or absence of disease that can regulate gut microbial composition. These are the parameters that can also be tweaked when medications are essential. 

The best way going forward is to look after your gut and give it a fighting chance to protect itself if you need to take any medications. 

Here are some suggestions you can put into place today.

Gut Performance™ heals, normalizes, and fortifies the protective lining of your digestive tract. It also contains prebiotics to help your naturally occurring microbiome to flourish.

Let us know via our Gut Performance ™ Instagram page if you have tried Gut Performance™ and if it has had an impact on improving your overall gut function!


de la Cuesta-Zuluaga, J., Mueller, N. T., Corrales-Agudelo, V., Velasquez-Mej, E., Carmona, J., Abad, J., & Escobar, J. (2017). Metformin is Associated with Higher Relative Abundance of Mucin-Degranding Akkermansia muciniphila and Several Short Chain Fatty Acid Producing Microbiota in the Gut Diabetes Care. Diabetes Care, 40, 54-62. doi:DOI: 10.2337/dc16-1324

Maier, L., Pruteanu, M., Kuhn, M., Zeller, G., Telzerow, A., Anderson, E., . . . Typas, A. (2018). Extensive impact of non-antibiotic drus on human gut bacteria. Nature, 555(7698), 623-628. Retrieved from

Weersma, R. K., Zhernakova, A., & Fu, J. (2020). Interaction between drugs and the gut microbiome. Gut, 69, 1510-1519. Retrieved from

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