The Most Dangerous Medications for Your Microbiome

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The community of microbes living in your gut, collectively known as the gut microbiome, are affected by many substances you place in your mouth including prescription medications.

Some medications like antibiotics are designed to kill pathogenic bacteria and other organisms but consequently, kill the “good” bugs as well. Other medications like corticosteroids reduce inflammation but also promote the growth of yeasts like candida leading to dysbiosis.

In fact, according to a study looking at over 1,000 commonly prescribed non-antibiotic medications, 24% are known to disrupt the growth of at least one species of bacteria in the microbiome. Imagine that for a moment: if you are taking a medication, there is a 24% chance that medication is affecting the diversity and composition of your gut microbiome, and that percentage increases with the addition of more medications.

Although the researchers tested non-antibiotic medications, many of the drugs exhibited antibiotic-like actions on the microbiome by inhibiting the growth of certain species of bacteria. This unexpected finding also suggests that non-antibiotic medications may promote antibiotic resistance. This is a very concerning discovery considering the troubles we are facing today with rising rates of antibiotic resistance. 

According to the German study and other research, the following types of medications can adversely affect the gut microbiome:

Antibiotics Can Wreak Havoc on Your Gut

From this list, antibiotics are the worst offenders as they are designed to kill off bacteria and/or prevent them from replicating. A major consequence of using antibiotics is that the “good” microbes in the gut are killed off in addition to the “bad” bugs.

Not all antibiotics are created equal though. Some antibiotics are more potent and have a broader spectrum – meaning they kill off many different types of bacteria. 

In a randomized placebo-controlled clinical trial, researchers from Europe looked at different classes of antibiotics and measured the loss of gut microbes from taking one dose. Here is what they found:

  • A single dose of clindamycin (a strong broad-spectrum antibiotic) caused a shift in the gut microbiome that took 4 months to return to baseline.
  • A single dose of Cipro (a strong broad-spectrum antibiotic) caused a shift in the gut microbiome that took 12 months or longer to return to baseline.
  • A single dose of amoxicillin (a less potent antibiotic) didn’t reduce the number or diversity of gut bacteria as much as clindamycin or Cipro did.

Of course, if you really need antibiotics, listen to your doctor and take them. If you do end up taking a potent antibiotic like Cipro, make sure that you are supporting your microbiome during and many months after the use of antibiotics to restore diversity and function.

Birth Control Pills and Your Microbiome

Birth control pills are used for many purposes including birth control, treatment of irregular periods, painful periods, and acne. They have helped millions of women but pose unwanted side effects. 

  • For women that have taken birth control for longer than 5 years, there is a three-fold increased risk is getting Crohn’s disease particularly those who are genetically susceptible.
  • Birth control pills are thought to affect colon permeability.
  • Birth control pills are thought to affect gut immunity.
  • Estrogen medications like birth control may directly impact the gut microbiome.

The take-home message here is if you are genetically more susceptible to gut issues like Crohn’s disease, you may want to talk to your doctor about alternative forms of birth control.

The Problem with Too Many Corticosteroids

Corticosteroids can be miracle drugs. I remember as a child I couldn’t breathe due to severe asthma, and many times had to go on prednisone to help clear up inflammation and open up my airways. To this day, if a patient needs to go on prednisone for a short period of time to reduce asthmatic symptoms, or reduce a severe outbreak of eczema, I unequivocally support this approach. 

Corticosteroids can be problematic though as they can lead to overgrowth of yeast or create dysbiosis. This generally only happens when they are taken in high doses for extended periods of time. 

Acid Blocking Medications Can Alter Your Gut

There are two main classes of acid-blocking medications used to treat heartburn, GERD, or ulcers:

H2 blockers block histamine from stimulating the stomach from producing acid.  They are less potent than proton pump inhibitors (PPI’s), and thus do not affect the gut microbiome as strongly as PPI’s do. 

PPI’s are quite strong and block acid production in the stomach. When acid production is suppressed, the pH of the stomach is altered and dysbiosis can occur. Other risks of taking PPI’s include the following:

  • Greater susceptibility to gastrointestinal infections like clostridium difficile
  • Reduction in the diversity of gut microbiome
  • Increased fracture risk

Fortunately, natural medicine offers many solutions to conditions like heartburn or GERD.  

How to Protect Your Gut from Medications

As you can see, there are many medications that affect the gut microbiome. If you plan on taking some of these medications for extended periods of time, there are many gut supportive treatments that can help re-establish a healthy gut microbiome. 

  • Take probiotics.
  • Eat fermented foods like sauerkraut, kimchi, pickled vegetables, etc.
  • Drink fermented drinks like kombucha, beet kvass, kefir, etc.
  • Eat prebiotic foods like garlic, onion, leeks, asparagus, artichokes, dandelion leaves, endive, or jicama.

Some simple lifestyle modifications can also improve the functioning on your gut and support the microbiome and these include:

  • Exercise
  • Stress reduction
  • Sound sleep
  • Reduction in use and exposure of chemicals

And if you are considering getting off some of your medications make sure you consult with an experienced and qualified doctor. Starting someone on medications is a lot easier than taking them off.  Many naturopathic, integrative, and functional medicine doctors will be able to help you reduce your pharmaceutical load.  

Dr. Drew Sinatra

Meet Dr. Drew Sinatra

Dr. Drew Sinatra is a board-certified naturopathic doctor and self-described “health detective” with a passion for promoting natural healing, wellness, and improving quality of life by addressing the root cause of illness in patients of all ages. His vibrant practice focuses on treating the whole person (mind, body, and spirit) and finding missed connections between symptoms and health issues that are often overlooked by conventional medicine.

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