Do medications affect gut health?

Many medications disrupt the natural flora and damage the gut lining. Those with antibacterial actions, such as antibiotics, certain cancer therapies, antihistamines, antipsychotics, antihypertensives, and antidepressants like SSRIs are particularly damaging. Sometimes changes are reversed when one stops taking the drug, but damage can persist for up to four years.

This article is for educational purposes only and is not intended for individual medical advice. it does not promote any changes in your existing prescription drug use without consult with your prescribing physician.

Drugs that affect the microbiome

Opioid based drugs trigger constipation, nausea, vomiting, and bloating. In the long term, can actually cause pain. Gut barrier dysfunction can lead to multiple food sensitivities and chronic inflammatory patterns such as headaches, joint pain, brain fog, and increased risk of infectious disease.

Pain blockers, in general, may lead to more pain, long term. Acute pain is needed to stimulate the lining of the gut to make protective mucus. Without it, gut health may deteriorate. Evidently, non steroidal anti-inflammatory (NSAID) drugs need to be used with caution- they affect the integrity of the gut lining. Ongoing use and administration of NSAIDs without food causes bleeding, inflammation, and ulceration in the stomach and small intestine.

Proton Pump Inhibitors (PPI’s) (drugs often ending in “-azole”) are used to lower stomach acid and thus they decrease enzyme release, risk B12 deficiency, and deplete factors of digestion. Extended PPI use causes polymicrobial small bowel bacterial overgrowth (SIBO) and is linked with celiac disease, C. difficile, diarrheal infection and contributes to bacterial resistance to antibiotics, including vancomycin (often used in antibiotic-resistant infections).

Metformin, used in diabetic patients, contributes to gut disruption that potentially increases risk of additional autoimmune disease.

Birth control pill and hormone replacement therapy depletes folic acid, vitamins B2,
B6, B12, C, and E, and the minerals magnesium, selenium, and zinc. The gastrointestinal inflammation increases the risk of developing Crohn’s disease by 50 percent. Increases risk of vaginal infection such as bacterial vaginosis, Trichonomiasis vaginalis, and Candida albicans (yeast) infections. These infections happen most during initial use of the contraceptive pill. It is believed the occurrence goes down over time.

Levothyroxine increases risk of small intestinal bacteria overgrowth (SIBO).

There’s more. It’s not just individual drugs that alter the microbiome; there is a compound effect. When one takes more than five drugs, there is a reduction in the overall healthy types of flora and an increase in troublesome bacteria such as H. pylori. or C. difficile. Additionally, when someone is on any particular drug(s), their gut favours those microbes that are required to metabolize (break down) the drugs.

Does that mean you stop the drugs? Not necessarily. You need to discuss the benefits versus the risks with your qualified healthcare provider, prescribing physician or pharmacist.

Bad gut health is more than a tummy ache.
It can be the root of many health issues.
Learn how to improve gut health and 
it will influence your entire being. 

Dr. Laura M. Brown, ND

Ask Dr. Laura about things you can do to help mitigate the unintentional gut damage caused by prescription medications.


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