The Missing Conversation About Medications and the Microbiome

It’s not something we want to think about, but we must.

Many people eventually end up on medications because they feel they have no other option. And when you’re sick or experiencing symptoms that interfere with your quality of life, you’ll often accept whatever help your doctor offers.

I was in that position two weeks ago.

As I mentioned last week, I had food poisoning that aggravated my stomach lining (gastritis). The food poisoning itself wasn’t the hard part. That was over within two days. The difficult part was what came afterward. My stomach wanted very little food, and I quickly became weak and tired.

After a week of this, I went to the doctor.

She prescribed an anti-nausea medication and a proton pump inhibitor (PPI), an acid-blocking medication commonly used for reflux and gastritis. I filled the prescriptions because I felt I was in no position to do otherwise. I was having trouble working, sleeping, and, of course, eating.

Given my holistic viewpoint, you may think I'm a bit of a hypocrite. But after my illness in 2023, which I worked so hard to recover from, I wasn’t interested in taking chances.

The anti-nausea medication didn’t concern me much, but the PPI did.

I know stomach acid plays an important role in digestion and healthy GI function. At the same time, gastritis is inflammation of the stomach lining, and I can understand why reducing acid exposure may help some people heal.

But at what cost?

A chance conversation with a microbiome microbiologist I know introduced me to something I didn’t know. He mentioned that PPIs have been associated with lower microbial diversity in the gut. Several studies have confirmed this.

The studies don’t always tell us how long people had been taking the medication before their microbiome was measured, but some evidence suggests these changes may begin within weeks.

Needless to say, I stopped both medications within a week and a half. I can’t say stopping them changed my symptoms in any way. My recovery has continued steadily.

Right now, my stomach feels pretty good as long as it isn’t empty. That’s common with gastritis. An empty stomach often brings back a gnawing sensation that is very uncomfortable. This is not my first experience with gastritis, but it's certainly the worst.

Years ago, I eventually discovered something that helped me with gastritis: a mixture of raw honey, turmeric, and black pepper, followed by a whole-milk chaser.

Say what you like, but it worked for me then, and it’s helping me now.

Raw honey may help soothe the stomach lining and provides antioxidants that support healing. Turmeric contains curcumin, which has anti-inflammatory properties. Black pepper improves curcumin absorption, and milk provides calcium and protein, which may help stimulate protective mucus production while temporarily soothing the stomach lining.

Together, the combination seems to reduce irritation and make my stomach more comfortable while it heals.

How did I arrive at this?

It started with golden milk, an Ayurvedic remedy for ulcers and gastritis, or so I was told. I’m certainly not an expert in Ayurveda.

Eventually, I decided turmeric ruined the taste of milk, so honey became the medium for the turmeric. I added black pepper to improve absorption and kept the milk as a chaser to preserve its benefits.

Sometimes I add cinnamon because it masks the taste of both the honey and turmeric, which is fine by me. Interestingly, animal studies such as this suggest cinnamon may also help support the stomach lining by reducing inflammation and promoting protective mucus production.

Perhaps I should add the cinnamon now and see if it helps even more.

I know this doesn’t constitute proof by scientific standards.

But it works for me.

And since I’m the one who is sick, that’s enough.

For me, that means no PPI and continuing my recovery.

Protecting my microbial diversity matters to me, and the ingredients in my little concoction also support the gut. Win-win.

But the bigger question is this:

A PPI is only one medication.

What about the others?

As it turns out, quite a few medications appear to affect the gut microbiome.

Antibiotics are the obvious example. Most of us understand they don’t just kill the bacteria causing an infection. They affect many other bacteria as well.

But researchers are now finding that numerous non-antibiotic medications may also alter the gut's microbial ecosystem.

Studies have linked changes in the microbiome to medications such as PPIs, metformin, antidepressants, NSAIDs, laxatives, statins, and even some blood pressure medications.

In 2018, researchers screened more than 1,000 medications and found that nearly one-quarter of drugs designed for human cells inhibited the growth of at least one strain of gut bacteria.

Think about that for a moment.

These medications had already been approved. Millions of people were already taking them. Yet their effects on the microbiome were largely unknown.

This isn’t because anyone was hiding anything. Until recently, we simply didn’t have the tools to study the microbiome in any meaningful way. But now we do.

For decades, drug safety focused on organs we could easily measure.

Does the drug affect the liver?

The kidneys?

The heart?

Does it interact with other medications?

Those are important questions.

But medications do not enter a sterile body.

They enter an ecosystem.

And that raises entirely new questions.

Should microbiome effects become part of the drug approval process?

Should medications intended for long-term use be evaluated for their impact on microbial diversity?

Should protocols be developed to help support the microbiome when these medications are necessary?

Because let’s be clear.

I’m not suggesting people refuse medications they need. I certainly didn’t even if it was only for 10 days.

But perhaps the conversation shouldn’t end with:

“Here is your prescription.”

Perhaps it should continue with:

“And here is how we can help support your microbiome while you take it.”

After all, we already monitor the liver, the kidneys, and bone health when medications are known to affect them.

Why should the microbiome be any different?

And think about this.

If we supported the body better while medications are being used, would those medications work better? Would there be fewer side effects?

Once we understand the effects a medication may have on the body, we can begin developing ways to protect against them.

That requires stepping outside the pharmaceutical model and recognizing that food, supplements, exercise, sleep, and lifestyle may all play a role in supporting the body, even when medications are necessary.

We’re not there yet.

But perhaps we should be.

PS: You may think that when trying to recover from physical eating, due to a lack of food, all you need to do is eat. Exercise is also needed to get back to where you were. It’s surprising how quickly the body starts to fall apart.