Medications That Affect Your Gut Microbiome & Long-Term Health - Lakeside Natural Medicine

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Medications That Affect Your Gut Microbiome & Long-Term Health

ByKatarina Meister, ND March 4, 2022

Regular or long-term use of certain medications can put you at risk for SIBO, otherwise known as small intestine bacterial overgrowth, as well as LIBO (large intestine bacterial overgrowth), IBS and other gut health issues. It is important to note that about 60-80% of people diagnosed with IBS actually have SIBO, (2). SIBO comes with a whole host of symptoms including excessive gas, abdominal bloating, abdominal pain, constipation, diarrhea, brain fog, fatigue, and so on.

For your long-term health and wellness it is important to look at regular medications you take as they could cause further harm down the road. Medications with the strongest associations with alteration of the microbiome include antibiotics, proton pump inhibitors, diabetic medications, laxatives, and NSAIDs. It is important to note that several other medications including antidepressants (SSRIs) and oral steroids have similar effects. For simplicity, let’s just focus on the top 5 biggest offenders.

The top 5 categories of medications that can harm the microbiome


Antibiotics work by eliminating all sources of bacteria. Depending on the type of antibiotic, some are more harmful than others. A meta-analysis took the top antibiotics prescribed in primary care and analyzed any induced gut microbiota, (3). A whopping 31 articles showed how antibiotics dramatically diminish the levels of bacteria diversity. The article also listed how most individuals can return to baseline after cessation of treatment; however, some studies suggest longer term dysbiosis close to 2-6 months post treatment. The two biggest broad spectrum antibiotic offenders include doxycycline and clarithromycin. Antibiotics that were shown to have little effect on the gut microbiome include phenoxymethylpenicillin, nitrofurantoin, and amoxicillin.

Doxycycline was shown to reduce, a beneficial bacterial species, Bifidobacterium diversity. Clarithromycin was shown to decrease the populations of Enterobacteria, Bifidobacterium sp and lactobacillus species for up to 5 weeks. Both Bifidobacterium species and Lactobacillus species carry many therapeutic benefits including enhancing gut barrier integrity, creation of B vitamins, creation of short chain fatty acids (SCFA) to feed good bacteria, modulating the immune system, inhibiting the colonization of pathogens (the bad bugs!), and aiding metabolism of carbohydrates.

Proton pump inhibitors

Proton pump inhibitors or PPIs  reduce stomach acid to alleviate heartburn. Data suggests that due to this mechanism, the lower stomach acid (hypochlorhydria) allows for colonization of pathogenic bacteria in the upper GI tract, (5). Specifically the overgrowth of predominately the opportunistic bacterium family, Streptococcaceae, was found among other species. Another study found PPI users were predisposed to C. Difficile infections.

Stomach acid acts as one of our innate immune mechanisms to protect our body from pathogens (bad bugs)! This is why having proper stomach is so important for your overall health. Often people with heartburn are suffering from low stomach acid, food sensitivities, or other gut dysbiosis such as SIBO.

Diabetes medications

Diabetic medications, such as metformin, have been found to affect the composition and function of microbiota, (11). Approximately 85.74 million Americans were prescribed metformin in 2019, and the numbers have only been rising over the last twenty years, (10). Escherichia coli was found to proliferate with metformin use. Most E. Coli can colonize the GI tract as normal flora; however, some strains have different virulence factors, or disease provoking capabilities. Possible symptoms associated with this medication and the resultant disruption of the microbiome are diarrhea, stomach cramping and vomiting.


Laxatives are often prescribed after gut issues have already developed, specifically gut motility issues or constipation. While they may alleviate motility issues or constipation in the short term, they can exacerbate gut dysbiosis in the long run. An over the counter laxative called MiraLAX, is the second largest digestive remedy in the United States, (9). This may explain why so many patients in my office are presenting with gut issues after chronic laxative use. Laxatives cause osmotic stress which create long term changes in the gut microbiota, disrupts the protective mucosal barrier along your GI tract from pathogens(bad bugs), and leads to disruption to a common commensal bacterium (the good bugs!). A better option for laxatives for constipation and motility issues are finding the root cause to the dysbiosis! Common causes of constipation are not eating enough fiber or drinking enough water. A good daily goal is to fill half your plate with vegetables and drink half your body weight in ounces of water. If that doesn’t do the trick further testing to rule out SIBO and other dysbiosis is important.


Microbial differences were shown in individuals taking NSAIDs versus those taking no medication. NSAIDs are one of the most frequently consumed pharmaceuticals in the world (1).  NSAIDs are commonly used for pain, but they are often also prescribed with proton pump inhibitors to alleviate heartburn. These different medication combinations further complicate the bacterial composition of the gastrointestinal tract. Therapeutic doses of NSAIDs can result in dysbiosis that drastically alters the gut microbiome. These changes have been shown to be dependent on the type of NSAID use, with more aggressive ones having worse outcomes on the gut microbiome.  


Medications have their place in health care and can offer lifesaving medical necessities and provide significant relief for your overall health. However, when thinking about your long-term health, it is important to avoid unnecessary medications to prevent gut dysbiosis or triggering SIBO down the road. This is where natural medicine shines! For most primary care concerns you can utilize naturopathic medicine. Naturopathic medicine has so many tools for heartburn, pain, GI motility issues (constipation), digestive support, and prevention of comorbidities such as diabetes. Naturopathic doctors also have the proper training to know when medications are indicated.


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Editor’s Note: The information in this article is intended for your educational use only. Always seek the advice of your physician or other qualified health practitioners with any questions you may have regarding a medical condition and before undertaking any diet, supplement, fitness, or other health program.

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