does prescription medication damage gut health?

Can prescription medication damage your gut health?

For years, I had a weekly migraine that lasted 3 days. It would take at least a day to recover, so over half my life was being spent in exhausted misery. Unsurprisingly, after suffering with these chronic migraines for about 5 years I became extremely depressed. My neurologist became concerned and referred me to a psychiatrist who prescribed nortriptyline (also known as Pamelor). This is an antidepressant that was approved back in 1964 that has been very well researched and widely prescribed. He said it could also reduce my migraine intensity and frequency along with lessening my feelings of depression. I was hopeful for the first time in years and looked forward to the prospect of something that could give me any modicum of relief.

And lo and behold, it did help! My mood and energy levels improved and although the migraine still mostly happened right on schedule, I felt less miserable overall. It was easier to get out of bed on Monday and I wasn’t having random crying spells during my morning shower. Other than a bit of a dry mouth I noticed no side effects. 

I was so focused on my improved mood that I didn’t pay much attention to the fact that I started having heartburn every morning after breakfast. LIke most people, I would occasionally get acid reflux after drinking too much alcohol and/or eating too much sugar or greasy fried foods but having daily heartburn for no apparent reason was something I had never experienced. After a couple weeks of driving to work in great discomfort, I tried to self diagnose via the internet and mostly saw people claiming that as you get older you simply have more trouble digesting. I was in my early 40s and thought “I guess I’m just older and weaker than I used to be” It never occurred to me in the slightest that the nortriptyline might be the cause. Over the next 6 years I would be on this medication and I became less and less able to digest most foods without major discomfort. Grains were the worst, and the smallest piece of any kind of bread would bring me fiery agony. In due course,  I mentioned my constant heartburn to both my neurologist and psychiatrist, but neither had any ideas or solutions other than to simply take an antacid. Taking antacids has become the norm for middle aged people and there is little concern as to why they are needed. It was to be assumed that as you age your gut becomes weaker somehow and so you just have to take Zantac or Prilosec and forget about it. However, I instinctively and deeply believed that not digesting properly was going to lead to other and perhaps worse health problems. And besides the constant stomach pain, I had gained 20 pounds despite not changing my diet at all. I developed a burning need to find out what was happening.

So I began my long trial of restrictive diets to try and help my situation. After many trials I found that eating a primarily paleo diet of meat and veggies seemed to cause the least amount of distress and so I basically ate that way for the next 6 years. If I ever ate toast, a sandwich or a piece of cake or a cookie I would suffer greatly and I began to believe that was going to be how it was for the rest of my life.

Thankfully that was not to be the case. My chronic migraines eased greatly (a story for another blog) and I made the decision to get off the antidepressants because I didn’t want to be dependent on them for life. I gradually weaned myself off over a three week period and although I had some unpleasant withdrawal symptoms, the improvement in my stomach was immediate and I soon realized that it was this medication that had been causing all my digestive issues. After a couple months off of the drug  my stomach was as healthy as it ever was in my 20s and 30s and I could once again eat bread without any problem at all. I couldn’t believe it. Why did this happen and why were my doctors so clueless? I had needlessly suffered for years. I was relieved, but also a bit angry and I wanted answers.

Initial google searches turned up a lot of results on how many medications were known to cause heartburn, including tricyclic antidepressants like nortriptyline can relax the lower esophageal sphincter and that is what they blame for the heartburn. However, other data indicates that they may contribute to heartburn by slowing the speed at which the stomach empties. But why?  What was the mechanism? I knew there must be a direct cause and effect, but that information was not being provided by the drug companies or doctors. I wondered if they even actually knew why themselves.

After a lot of digging I believe I have found a likely answer. What I learned is that many, many medications actually kill your gut bacteria outright and that negatively impacts your microbiome and that is what causes improper digestion and the resulting heartburn. This seemed like a very simple and direct answer and I had to wonder why it was so hard to discover this information and why neither of my doctors seemed informed on the topic. But then again, maybe it isn’t so mysterious considering the behemoth of big pharma. Take a drug for one condition and then you must take another drug to combat the side effects of the first and then perhaps you might need even another drug to combat those side effects, and so on. For the current medical establishment it appears that the human microbiome is pretty much off the radar almost entirely. My doctors appeared unaware of the role of nutrition and gut health’s impact on digestion and the relationship to overall health.

How many medications kill gut bacteria? 

The first medications I learned killed gut bacteria was, naturally, antibiotics. This is well known and makes sense since an antibiotic doesn’t differentiate between good and bad bacteria. However, what was shocking to learn is that more than one-quarter of non-antibiotic medicines inhibit the growth of bacteria in the human gutSource. In a recent 2018 study, “Researchers at the European Molecular Biology Laboratory, in Germany, tested about 1,000 medicines on 40 species of gut bacteria. Of 923 non-antibiotics tested, 250 affected the growth of at least one of species of gut bacteria.” Source

Although this research definitively shows that at least a quarter of non antibiotic drugs kill gut bacteria, the process is not understood. In the study, research team member, Kiran Patil states, “This is just the beginning. We don’t know yet how most of these drugs target microbes, how these effects manifest in the human host, and what the clinical outcomes are. We need to carefully study these relationships, as this knowledge could dramatically improve our understanding and the efficacy of existing drugs.” Source

I had a hard time believing that nobody had any idea as to why all these non antibiotic drugs caused the destruction of gut bacteria. And sure enough, by digging deeper I was able to find 3 most likely causes.

Magnesium stearate?

One of the possible causes could be magnesium stearate. This substance is used in virtually all manufactured drugs as a “flow agent,” something which helps ensure that the equipment runs smoothly and the various ingredients stay blended together in the correct proportions. It is composed of magnesium and stearic acid, and oftentimes, palmitic acid as well. It is commonly noted in medical literature that magnesium stearate decreases the absorption rates of tablets and capsules by coating a good portion of the molecules in a tablet or capsule, it requires digestive enzymes to break down the magnesium stearate coating before the chemicals it envelopes are made available for absorption in order to reduce the absorption rate. A study demonstrates that stearates reduce the dissolution rate of capsules by 65% Source. This is most concerning to individuals with already existing digestive issues that impair nutrient absorption, such as Leaky Gut Syndrome, SIBO, Crohns, Ulcerative Colitis and other gut issues. Magnesium stearate may also irritate the bowel mucosal lining, causing digestive issues, such as chronic diarrhea. Most of the available information though insists that stearates are completely safe and some claim that they are actually good for you. If the mainstream medical system actually paid attention to gut health and the microbiome I might be more likely to take their word on this, but since they seem largely ignorant I must take their claims with a grain of salt.


Emulsifiers are found in many processed foods, not just medications. Studies have shown that the consumption of emulsifying agents results in microbiota encroachment into the mucus, alterations in microbiota composition, and development of chronic inflammation. For detailed information read the study entitled “Dietary emulsifiers directly alter human microbiota composition and gene expression ex vivo potentiating intestinal inflammationSource

Gastric Mucosal Barrier

The gastric mucosal barrier is the property of the stomach that allows it to safely contain the gastric acid required for digestion. If the barrier is broken, acid diffuses back into the mucosa where it can cause damage to the stomach itself.  It has been well documented that NSAIDs (non steroidal anti-inflammatory drugs) damage the gastric mucosal barrier and the human microbiome in this way. Source.  Other drugs including corticosteroids also are documented to have this effect Source It is likely that other drugs also damage the mucosal barrier but have yet to be studied or documented. 

Conclusions/What can I do?

Science is showing that not just antibiotics, but many medications damage gut health. The consequences of which can lead to a host of other seemingly unrelated problems. So what is the answer? If at all possible, ditch the pills and find another way to deal with your medical issue. If your condition makes it impossible for you to quit the pills then you can at least try to boost your guts microbiome. 

You can improve your microbiome primarily by eating the right foods. Fermented foods like sauerkraut and other fermented veg help your gut immensely. Also prebiotic rich plants like garlic, onions, apples and oats. Cruciferous vegetables like kale, cabbage and broccoli. Immediately stop eating processed foods and anything containing artificial sweeteners. Exercise and proper sleep are also a must.

Digestive Bitters?

Digestive bitters are a formula of bitter herbs that support digestive function by stimulating digestive juices, bile, and enzymes so that we can break down food naturally. Digestive bitters sold by Cordial Organics are enhanced with CBD for extra gut health.  We currently have 5 different digestive bitters you can try. Use coupon code GUTBLOG2021 to receive 20% off any Cordial Organics bitters.

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