Impact of commonly used drugs on the composition and metabolic function of the gut microbiota

Arnau Vich Vila, Valerie Collij, Serena Sanna, Trishla Sinha, Floris Imhann, Arno R. Bourgonje, Zlatan Mujagic, Daisy M. A. E. Jonkers, Ad A. M. Masclee, Jingyuan Fu, Alexander Kurilshikov, Cisca Wijmenga, Alexandra Zhernakova and Rinse K. Weersma ()
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Arnau Vich Vila: University of Groningen and University Medical Center Groningen
Valerie Collij: University of Groningen and University Medical Center Groningen
Serena Sanna: University of Groningen and University Medical Center Groningen
Trishla Sinha: University of Groningen and University Medical Center Groningen
Floris Imhann: University of Groningen and University Medical Center Groningen
Arno R. Bourgonje: University of Groningen and University Medical Center Groningen
Zlatan Mujagic: Division Gastroenterology Hepatology, Maastricht University Medical Center
Daisy M. A. E. Jonkers: Division Gastroenterology Hepatology, Maastricht University Medical Center
Ad A. M. Masclee: Division Gastroenterology Hepatology, Maastricht University Medical Center
Jingyuan Fu: University of Groningen and University Medical Center Groningen
Alexander Kurilshikov: University of Groningen and University Medical Center Groningen
Cisca Wijmenga: University of Groningen and University Medical Center Groningen
Alexandra Zhernakova: University of Groningen and University Medical Center Groningen
Rinse K. Weersma: University of Groningen and University Medical Center Groningen

Nature Communications, 2020, vol. 11, issue 1, 1-11

Abstract: Abstract The human gut microbiota has now been associated with drug responses and efficacy, while chemical compounds present in these drugs can also impact the gut bacteria. However, drug–microbe interactions are still understudied in the clinical context, where polypharmacy and comorbidities co-occur. Here, we report relations between commonly used drugs and the gut microbiome. We performed metagenomics sequencing of faecal samples from a population cohort and two gastrointestinal disease cohorts. Differences between users and non-users were analysed per cohort, followed by a meta-analysis. While 19 of 41 drugs are found to be associated with microbial features, when controlling for the use of multiple medications, proton-pump inhibitors, metformin, antibiotics and laxatives show the strongest associations with the microbiome. We here provide evidence for extensive changes in taxonomy, metabolic potential and resistome in relation to commonly used drugs. This paves the way for future studies and has implications for current microbiome studies by demonstrating the need to correct for multiple drug use.

Date: 2020
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DOI: 10.1038/s41467-019-14177-z

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