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Drugs That Affect The Gut Microbiome

We all  know that antibiotic affect our microbiome, however, also other drugs, such as statins and antidepressants, have a profound impact on our microbial communities.

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Our gut microbiome plays a major role in the production of vitamins, enzymes and other compounds that digest and metabolize food ad regulate our immune system. The gut microbiome is considered as an extra organ with a remarkable complex ecosystem. The gut microbiota is not static but changes over time as a consequence of a large number of host and environmental factors. Pharmacological interventions such as antibiotic therapy are well known to disturb the balance of the gut microbiome. 



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Antibiotics have become one of the cornerstones in the prevention and treatment of infectious diseases. However, their use is not without side effects as it may lead to long term disturbances of the intestinal microbiota. There is growing evidence that these antibiotic induced perturbations of the microbiota play an important role in a multitude of disorders like irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), allergy and colorectal cancer1-4. In addition, the antibiotic induced disturbance of the microbiota can lead to the overgrowth of potential pathogens like Clostridium difficile which may result in a serious or life-threatening infection.


Recently, a study was published presenting a systematic metagenomics association analysis of 207 intrinsic and exogenous factors5. The  study used data from 1179 participants in the LifeLines-DEEP cohort, a Dutch population-based study. The researchers tested 20 factors with respect to the microbiomes of these participants among which 44 categories of drugs.

Drugs associated with interindividual variation of gut microbiome. The bar plot indicates the explained variation of each factor in the interindividual variation of microbial composition [Bray-Curtis (BC) distance]. The heatmap next to the bar plot shows the correlation coefficients of each factor with Shannon’s index of diversity, gene richness, and COG richness, respectively. Color key for correlation is shown.


Source: Zhemakova A., Kurilshikov A., Bonder M.J., et al. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science 2016 29;352(6285):565-9.

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As can be expected, the use of antibiotics was significant associated with microbiome composition. However, not only anitbiotics, but also PPI’s, antidepressants, statins and other commonly used medication were associated with distinct gut microbiota signatures. As a consequence, commonly used medications could affect how the gut microbiota resist enteric infections, promote or ameliorate gut inflammation, or change the host's metabolism6





Proton pump inhibitors (PPIs) are among the top 10 most widely used drugs in the world. PPI use has been associated with an increased risk of enteric infections, most notably Clostridium difficile7.

Given the widespread use of PPI and anitbiotics, the morbidity and mortality associated with enteric infections, and the increasing number of studies investigating the microbiome, healthcare practitioners and microbiome researchers should be fully aware of the influence of drugs on the gut microbiome.

Read the scientific article 


1. Dethlefsen L, Eckburg PB, Bik EM, et al. Assembly of the human intestinal microbiota. Trends Ecol Evol 2006;2: 517-523.          

2.Othman M, Aguero R, and Lin HC. Alterations in intestinal microbial flora and human disease. Curr Opin Gastroenterol 2008;24:11-16.

3. Penders J, Stobberingh EE, van den Brandt PA, et al. The role of the intestinal microbiota in the development of atopic disorders. Allergy 2007;62:1223-1236.

4.       Shreiner A, Huffnagle GB, and Noverr MC. The "Microflora Hypothesis" of allergic disease. Adv Exp Med Biol 2008;635:113-134.

5.  Zhemakova A., Kurilshikov A., Bonder M.J., et al. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Scinece 2016 29;352(6285):565-9.

6 . Imhann F., Vila A.V.,, Bonder M.J., et al.. The influence of proton pump inhibitors and other commonly used medication on the gut microbiota. Gut Microbes Vol. 0 , Iss. 0,0

7. Imhann F, Bonder MJ, Vich Vila A, et al. Proton pump inhibitors affect the gut microbiome Gut Published Online First: 09 December 2015. doi: 10.1136/gutjnl-2015-310376




Drugs that affect our microbione

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