Clean Living

These medications could be affecting your gut health...

These medications could be affecting your gut health...

It's hard to imagine, but as little as 75 years ago, any number of easily-treatable health conditions could quickly turn serious. We've been incredibly fortunate to live in a different era since the development of antibiotics in the 1940s, and it's truly amazing that we have effective, life-saving medicines for so many bacterial conditions that were previously deemed untreatable.

However, we're now far enough into the antibiotic age that we're finally able to see the implications of widespread antibiotic use, and it's not a pretty picture. You see, antibiotics are best thought of as a last resort to be used only when absolutely necessary, but we've come to see them as a first resort and even a prophylactic measure, which has had some serious effects on our health and our microbiomes.

An Antibiotic Problem

We've known for a long time that antibiotics kill bacteria indiscriminately, which is bad news for the gut microbiome and your overall health. To truly understand the devastating effects this can have on your body, picture your gut microbiome like a garden.

When you have a wide variety of beneficial plants, the soil benefits, the good plants can crowd out the weeds, and the whole ecosystem thrives. But if you pour gas on the garden and burn it down, the effects last much longer than the fire. Once the flames die down, the weeds have a prime opportunity to quickly move in and take over the whole space, crowding out any good plants that are trying to grow again. Unless you take specific measures to go in and rehabilitate the garden, repopulating it with beneficial plants and giving them the nourishment they need to grow and crowd out the bad guys, you've got a recipe for a weed-choked lot.

Taking antibiotics creates roughly the same effect in your gut: by killing off all the bacteria indiscriminately, it creates conditions that allow undesirable bacteria to thrive for a long time afterwards. Indeed, just one course of antibiotics can negatively affect your gut for up to a year.1

While the trend of overprescribing antibiotics for every little thing is (thankfully) starting to die down in favor of more preventative, natural care, we're still more exposed to antibiotics through food and medication than is ideal––and new research is showing that we should beware of other medications’ effects on the microbiome as well.

The Bad News: How Medication Affects the Microbiome

A comprehensive study from the European Molecular Biology Laboratory (EMBL) examined the effects of over 1,000 medications on 40 bacterial strains, and found that even non-antibiotic medications have some serious, potentially harmful effects on the composition of your gut microbes.2

When researchers tested the medications, they found that more than 800 “human targeted drugs” not designed to interact with the gut microbiome at all had antibacterial effects, with 40 medications reducing the numbers of over 10 different strains of bacteria. And shockingly, more than a quarter of the 923 non-antibiotic drugs hindered the growth of at least one strain of gut bacteria!

Several types of commonly-prescribed medications that seemed to have particularly serious effects on bacteria include chemotherapy drugs and calcium channel blockers. Other microbiome-busting medications were:

• Proton Pump Inhibitors: Commonly prescribed acid-reducing medications for promoting easy digestion and getting rid of that burning feeling in your chest have been shown to both significantly decrease the overall diversity of your gut microbiome and increase the number of certain unwanted species, including C. difficile, Streptococcus, Staphylococcus, and E. coli.3,4

• Atypical Antipsychotics: Specific types of medications used to help with low mood, mood swings, and anxious thoughts appear to interact heavily with the gut microbiome, potentially reducing the overall number of bacteria in the gut and shifting the profile of the gut microbiome to the types of bacteria that facilitate weight gain.5

• Non-Steroidal Anti-Inflammatory Drugs: Research shows that taking over-the-counter medications for things like a pounding head, an achy back, or bouts of temporary inflammation—such as from exercise—can cause an increase in species you'd rather not have in your gut microbiome, including Pseudomonadaceae, which are associated with upper respiratory conditions that can leave you in bed for a month, skin problems, and ENT issues. And, these medications can damage your gut lining, letting unwanted bacteria move in and set up shop more easily.6,7

What's more, researchers found that some bacteria actually develop a resistance to non-antibiotic medications similarly to how they do with antibiotics, meaning that we've likely been contributing to widespread antibiotic resistance without realizing it—just by utilizing common, everyday medicines.

The Good News: The Role of Bacteria in Treatment

While all of that is definitely a downside, the EMBL study also opens the door for some really interesting changes in the way we treat conditions. The study sheds light on the previously-unknown working relationship that some medications have with the gut microbiome. In fact, in some instances it looks like gut bacteria are actually doing a portion of the heavy lifting we ascribed to medications! For instance, research indicates that certain medications used to normalize blood sugar actually appear to only really work well in the presence of beneficial bacteria and the short-chain fatty acids they produce.8

Similarly, the relationship between bacteria and mental health medications may explain why some of these medicines take a couple of weeks to kick in. It appears that the medications work in part because of their effects on the gut microbiome, which makes sense given that your gut microbiome has a direct line to your brain via the gut-brain axis, and plays a huge role in supporting the production and balance of your hormones.9

By further understanding how medications work with bacteria, we can optimize them to be more effective treatments that make the most of their bacterial allies.

Moving Towards Microbiome-Specific Healthcare

Researchers in the study also found that everyone's gut microbiome is quite distinct to them, which means that if we can get a really clear sense of what's going on in someone's microbial mix, we may be able to tailor medical treatments to match people's microbiomes.

The researchers acknowledged that this level of sophistication may be a while off, given how many factors affect the gut microbiome and how quickly its composition can change, but they also noted that there were universal changes in microbial composition that stayed true across multiple people, meaning that even if we can't crack the code of individualized microbial treatments, we've still got a lot of potential for incorporating beneficial bacteria in healthcare.

Ultimately, your bacteria are your best bet for maintaining your overall health––they interact with your body from head to toe, including factors you'd never even think could be connected with your gut, like your sleep cycles, weight management, immune function, and skin. Studies like this make it even clearer just how important it is to support your bacterial health with just as much focus as you do any other aspect of your well-being. So make sure that you're doing what you can to maintain an appropriate balance of bacteria in your gut, like moving regularly, drinking lots of water, and opting for natural, non-invasive approaches that will be as gentle on your body (and your microbes!) as possible.

Love Your Gut With Probiotic Support

That being said, chances are that sometimes you're going to need to take medications, but this doesn't mean that all your gut-friendly efforts have to go to waste! Whenever you do need to take medicines––especially if they're antibiotics or have antibacterial effects––give your bacterial allies some extra support with high-quality probiotic and prebiotic supplementation, so your microbiome can retain its delicate balance.

PRO-15 is formulated with 15 targeted strains to replenish your gut with beneficial bacteria, and Prebiotic Powder contains the perfect mix of prebiotic fiber that helps your good guys need thrive. In combination, this dynamic duo (available together in the Digestive Starter Pack) is ideal for offering your gut some bacterial TLC after medication-related depletion, as well as maintaining a healthy balance of bacteria to keep you feeling good so you may not have to take bacteria-lowering medications in the first place.

Because ultimately, that's what it's all about: staying healthy. There truly is no better way to support optimal health than by working with your microbiome, so go with your gut––avoid unnecessary medications, give your body continuous support to stay well instead of opting for invasive interventions, and make a commitment to support the bacterial allies that keep you feeling good and looking great!


1. Zaura, E., Brandt, B. W., Mattos, M. J., Buijs, M. J., Caspers, M. P., Rashid, M., . . . Crielaard, W. (2015). Same Exposure but Two Radically Different Responses to Antibiotics: Resilience of the Salivary Microbiome versus Long-Term Microbial Shifts in Feces. MBio, 6(6). doi:10.1128/mbio.01693-15

2. Maier, L., Pruteanu, M., Kuhn, M., Zeller, G., Telzerow, A. . . . Typas, A. (2018). Extensive impact of non-antibiotic drugs on human gut bacteria. Nature, 555, 623–628. doi: 10.1038/nature25979

3. Imhann, F., Bonder, M.J., Vich Vila, A., Fu, J., Mujagic, Z. . . . Zhernakova, A. (2016). Proton pump inhibitors affect the gut microbiome. Gut 65(5), 740-8. doi: 10.1136/gutjnl-2015-310376

4. Jackson, M.A., Goodrich, J.K., Maxan, M.E., Freedberg, D.E. . . . Steves, C.J. (2016). Proton pump inhibitors alter the composition of the gut microbiota. Gut 65(5), 749-56. doi: 10.1136/gutjnl-2015-310861

5. Morgan, A.P., Crowley, J.J., Nonneman, R.J. . . . Sullivan, P.F. (2014). The Antipsychotic Olanzapine Interacts with the Gut Microbiome to Cause Weight Gain in Mouse. PLoS ONE 9(12). doi: 10.1371/journal.pone.0115225

6. Rogers, M.A.M., Aronoff, D.M. (2016). The influence of non-steroidal anti-inflammatory drugs on the gut microbiome. Clinical Microbiology and Infection, 22(2), 178.e1-178.e9. doi: 10.1016/j.cmi.2015.10.003

7. Otani, K., Tanigawa, T., Wantanabe, T., Shimada, S., Natadani, Y. . . . Arakawa, T. (2017). Microbiota Plays a Key Role in Non-Steroidal Anti-Inflammatory Drug-Induced Small Intestinal Damage. Digestion, 95(1), 22-28. doi: 10.1159/000452356

8. Forslund, K., Hildebrand, F., Nielsen, T., Falony, G. . . . Pederson, O. (2015). Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature, 10;528(7581), 262-266. doi: 10.1038/nature15766.

9. Flowers, S.A., Evans, S.J., Ward, K.M., McInnis, M.G., Ellingrod, V.L. (2017). Interaction Between Atypical Antipsychotics and the Gut Microbiome in a Bipolar Disease Cohort. Pharmacotherapy, 37(3), 261-267. doi: 10.1002/phar.1890


Rachel Allen is a writer at Hyperbiotics who's absolutely obsessed with learning about how our bodies work. She's fascinated by the latest research on bacteria and the role they play in health, and loves to help others learn about how probiotics can help the body get back in balance. For more ideas on how you can benefit from the power of probiotics and live healthier days, be sure to subscribe to our newsletter. To learn more about how a healthy microbiome can enrich your life, subscribe to our newsletter.