Gut Flora

How conventional medications can impact your gut function

I’m a naturopath for a reason – and one of those reasons is that natural remedies have less side effects than the majority of industrially made pharmaceuticals.

One of the less-known impacts of pharmaceuticals is that many of them impact your gut function. That’s why when we have a consultation I ask what your medications are. I’m not being nosy, I’m checking for side effects and ensuring that what I prescribe is truly complementary – and safe for you.

Both prescription medications and over-the-counter products can have non-trivial side effects.

This is also NOT just my opinion – there are an increasing number of clinical studies confirming these impacts.

Some common gut-impacting medicines – and the evidence of their impact

There are currently more than 20,000 approved drugs being used around the world. (A list of the studies confirming their side effects would be way more than a blog post.)

But some short examples of type of drugs and the kinds of impact they could have on your gut could be useful..


Antibiotics were designed to kill bacteria – all sorts of bacteria. So they can often affect your gut bacteria – because that is their job. But regular or long-term use can easily make you susceptible to gut function problems like SIBO (Small Intestinal Bacterial Overgrowth), LIBO (Large Intestinal Bacterial Overgrowth), IBS (Irritable Bowel Syndrome) and other gut health issues. (This study documents such impacts: PMID: 32958481).

Proton pump inhibitors

Proton-pump inhibitors (PPIs) like Losec, Nexium and Pariet often prescribed for reflux do serve the purpose of reducing stomach acid – but that can easily inhibit the healthy function of your gut flora. (This study documents such impacts: PMID: 31990420).

Diabetes medications

Diabetes medications like metformin have been found to affect both the makeup and efficiency of your gut flora (This study documents such impacts: PMID: 31953381). In particular E. coli can be allowed to proliferate during metformin use.


And laxatives, while sometimes needed when gut issues have already developed and caused constipation, can actually exacerbate gut dysbiosis (This study documents such impacts: PMID 32409589). If constipation and motility are issues impacting you, get advice from your health practitioner.

Drugs aren’t “safe” – just helpful in the right context

There are many other medications that have similar effects but the above four groups are considered the leading offenders.

Some medications can’t be avoided and can certainly be life-saving or life-improving. It’s a matter of balance and understanding the benefits and risks.

Wherever you can, it is worth:

  • avoiding pharmaceutical medications
  • getting expert advice on naturopathic alternatives and
  • making a real effort with lifestyle changes.

The easy options are NOT risk free – and may be having unrecognised impacts on your gut – and hence your entire immune system response. (The last thing you need in the midst of a global pandemic.)

So even if you aren’t aware of gut problems, if you’re on long term pharmaceuticals then talk to your friendly local naturopath.

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