Medication's Impact on the Gut Microbiome

Medication's Impact on the Gut Microbiome

  • Gut Health

  • By Jef L’Ecuyer, Registered Dietitian

    More and more often, we’re learning about the importance of the connections between the health of the gut microbiome and the overall health and wellbeing of our bodies.

    We already know how we treat our bodies; how we move it, how much sleep we have, and how much stress we deal with - all impact our gut health. We also know that what we put into our bodies; including food, supplements, and medications has a huge impact as well.


    Medications & Gut Bacteria

    Many of us know that taking antibiotics, even if necessary, can negatively impact our digestive health, particularly our gut microbiome, but not everyone is aware of the impacts of other medications. Common prescriptions that can be immensely helpful to our wellbeing are not always helpful for our guts.

    Surprising new research is showing us that nearly 1 in 4 non-antibiotic drugs can inhibit the growth of certain bacterial strains within the human gut. Beyond the common detrimental effects of an altered microbiome as a result of dysbiosis, what’s even more alarming is that of the over 1000 marketed drugs that were tested, many may also promote antibiotic resistance1.


    Antibiotics: A Quick Review

    Antibiotics destroy microorganisms by nature. While proven effective for many conditions, and life-saving at times, the problem is that they don’t discriminate what they kill. That is, they kill the pathogenic bacteria (aka the bad guys), but they also clear out the good guys too. This disruption leads to a vulnerable state and potentially to dysbiosis which then leads to the possibility of a variety of other more serious health concerns.

    For now, the good news is that with more awareness around the side effects of antibiotics, people are more knowledgeable and will ask to learn more from their health care professional. However, with more and more evidence coming to light about how many other meds (generally thought to be safe) can impact the gut, it's becoming increasingly important to learn about the effects of the drugs and weigh the pros/cons you and your loved ones are prescribed.



    “Protein Pump Inhibitors” (PPIs) are a group of widely-used drugs whose main action is to reduce the levels of stomach acid production in the body. They are used for treating a wide range of gastro-esophageal conditions such as heartburn, GERD and the prevention of gastric ulcers. Although these drugs are widely seen to be safe, recent studies show their use has a probable association with the alteration of the gut microbiome, including associations with an increased risk of enteric infections, most notably Clostridium difficile.2



    Non-steroidal anti-inflammatory drugs (NSAIDs) are a highly prescribed class of medications known for treating a variety of conditions including reducing fevers, reducing pain, prevention of blood clots and when used in larger doses, for help to reduce inflammation.

    Many NSAIDs are familiar, over-the-counter remedies such as aspirin and ibuprofen, and yet despite their widespread use and availability, they do have impacts on the bacteria found within the gut microbiome. NSAIDs have been known to cause damage to the small intestine, putting users at risk for ulcers. It’s further known that the gastrointestinal tracts, including the microbiomes of individuals, reflect the combinations of medications that they have ingested3.


    Oral Contraceptives

    Oral Contraceptives, more commonly known as birth control pill, is highly effective at pregnancy prevention, endometriosis, managing painful periods amongst other uses cases involving hormonal imbalances. Although the current research is more limited in this area, emerging studies are showing links between problems in gut-related conditions.

    One study focused on (genetically predisposed) women who have taken exogenous hormones for extended periods of time, associated with high rates of flare-ups of Crohn's disease (a chronic inflammatory disorder of the gastrointestinal tract). Once again, we see here that common use of widespread medications is impacting the gut health of those using them. The authors say: “Although the exact mechanism underlying this association is unclear, the effect is plausibly mediated by alterations in intestinal permeability, immune function, and, potentially, the gut microbiome”. 4


    Iron Supplementation

    Oral iron supplementation is a common way to replenish iron stores when low and is used often in the case of iron deficiency anemia. Despite this, there have been many reported adverse effects on the gut. Because iron is not easily absorbed by the body, some researchers theorize that excess iron may cause a shift towards a more "pathogenic profile" of bacteria within the intestine through the promotion of the growth of pathogenic strains. For this reason, it is always advised not to self-prescribe iron supplementation.


    So...What Can You Do?

    As with any new supplement or medication, it is always a good idea to have a frank and open discussion with your health care professional about the side effects of both. If the benefits of the medication outweigh the negative side effects, it's helpful to ask if there is a way to lessen or space out the dose. Lifestyle changes can also help reduce negative impacts on the gut!


    You can support your health when faced with the need for medications using alternative or functional approaches to health condition. There are plenty of herbal options, natural foods and lifestyle practices that can be helpful for common ailments. Supporting your gut microbiome with the healthy bacteria of a high-quality probiotic, on an ongoing basis, will also help to prevent the negative consequences of any outside environmental influences, including the negative effects of various medications.


    Do you have any other questions about gut health? Ask us in comments below. If you are looking to stock up on Bio-K+, head to our store locator. For more information on Bio-K+, probiotics and digestive health, contact us, find us on Facebook and Instagram or join our community




    1. Maier, L., Pruteanu, M., Kuhn, M., et al. Extensive impact of non-antibiotic drugs on human gut bacteria. Nature, published online 19 March. DOI: 10.1038/nature25979

    2. Takagi T, Naito Y, Inoue R, et al. The influence of long-term use of proton pump inhibitors on the gut microbiota: an age-sex-matched case-control study. J Clin Biochem Nutr. 2017;62(1):100-105.

    3. Rogers MAM, Aronoff DM. The influence of non-steroidal anti-inflammatory drugs on the gut microbiome. Clin Microbiol Infect. 2015;22(2):178.e1-178.e9.

    4. Khalili H, Granath F, Smedby KE, et al. Association Between Long-term Oral Contraceptive Use and Risk of Crohn's Disease Complications in a Nationwide Study. Gastroenterology. 2016;150(7):1561-1567.e1.


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    Jef L’Ecuyer Registered Dietitian
    About the author
    After her nutrition training at McGill University, Jef specialized in gastrointestinal health with a special interest in the microbiota and Irritable Bowel Syndrome. With Bio-K+, she continues on this path by making the world of probiotics more accessible to all.
    View all articles by Jef L’Ecuyer
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