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It’s Not Just Antibiotics that Potentially Harm Gut Health

It’s Not Just Antibiotics that Potentially Harm Gut Health

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Which of these prescription medications are YOU taking?

Most people are aware that antibiotic medications can alter the balance of good and bad bacteria in the gut. In addition to the science we have proving this, many of us have personally experienced upset bellies and changes in stool patterns upon taking an antibiotic.

However, many people do not know that many other categories of commonly prescribed drugs – not just antibiotics – can also alter our microbial health. This includes medications that have therapeutic effects directed at the gastrointestinal tract such as proton pump inhibitors,[1] as well as anti-diabetic medications,[2] statins,[3] antidepressants, non-steroidal anti-inflammatory drugs (NSAIDs),[4] and atypical antipsychotics.[5] Many patients use these types of medications on an ongoing basis. With our increasing knowledge of how our gut microbiome affects our mood,[6] metabolism,[7] immune system function and more,[8],[9] it is imperative that we look further at how we are altering its normal balance, as well as if supportive strategies such as probiotics should be inherently recommended when we elect to use these additional types of medications, especially long-term.

Proton pump inhibitors

Although antibiotics are often blamed for the increased incidence of Clostridium difficile, a bacteria that can cause a life-threatening infection in the intestines, the use of proton pump inhibitors (PPIs) also is a contributing factor.[10] Multiple systemic reviews have shown an association between the use of medications that suppress stomach acid production and increased risk of gastrointestinal infections.[11],[12] PPIs are among the most common prescriptions in the world, including in children.[13],[14] By reducing stomach acid production, PPIs allow for the survival of harmful bacteria that otherwise would not survive the harsh acidic environment of the stomach.[15] Users of PPIs have also been shown to have a significantly different composition of microbes in the gut than non-PPI users.[3]

Interestingly, probiotics have been shown to significantly reduce the incidence of colic and reflux in infants,[16] as well as upper gastrointestinal symptoms like reflux in adults,[17],[18] leading many integrative practitioners to use this as an adjunctive or alternative first-line intervention.


Metformin is recommended as the first-line intervention for patients newly diagnosed with type 2 diabetes mellitus (T2DM), or insulin-resistant diabetes. As approximately 10 to 15% of the US population has T2DM, the number of individuals using this medication, at least during some period of the course of this often-chronic illness, is almost as high as the prevalence of the disease itself. Metformin has been demonstrated to inhibit the growth of Bifidobacterium longum,[19] a “good” type of bacteria commonly found at high numbers in the human gut.[20] Treatment of T2DM with metformin has also been shown to lead to a significant increase of Escherichia spp. (like E. coli), as well as other changes to the microbial balance.[21]

Atypical antipsychotics

Metabolic side effects are commonly associated with the use of atypical antipsychotic medications, but the mechanisms of these changes are largely not understood. In women being treated with these medications, a significantly decreased species diversity of the gut microbiome has been observed.[6] Decreased levels of bacterial species diversity, such as seen here, is one of the things which have been seen with obesity,[22] and may be a contributing factor in this medication-treated group as well.


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The information provided is for educational purposes only. Consult your physician or healthcare provider if you have specific questions before instituting any changes in your daily lifestyle including changes in diet, exercise, and supplement use.

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