TY - JOUR
T1 - Impact of commonly used drugs on the composition and metabolic function of the gut microbiota
AU - Vila, A.V.
AU - Collij, V.
AU - Sanna, S.
AU - Sinha, T.
AU - Imhann, F.
AU - Bourgonje, A.R.
AU - Mujagic, Z.
AU - Jonkers, D.M.A.E.
AU - Masclee, A.A.M.
AU - Fu, J.Y.
AU - Kurilshikov, A.
AU - Wijmenga, C.
AU - Zhernakova, A.
AU - Weersma, R.K.
N1 - Funding Information:
We would like to thank all participants from the three cohorts used in this study for providing their phenotypes and stool samples: LifeLines DEEP, the UMCG IBD cohort and the Maastricht University Medical Center IBS cohort. Furthermore, we thank B.H. Jansen for logistic and laboratory support and the IBD nurses at the UMCG IBD clinic, M.A.Y. Klaassen and L. Bolte, for patient inclusion and collection of the samples. We also thank K. McIntyre, who is employed by the Department of Genetics, UMCG, for English and scientific editing services. R.K.W., A.Z. and J.F. are supported by VIDI grants (016.136.308, 016.178.056 and 864.13.013) from the Netherlands Organization for Scientific Research (NWO). R.K.W. is further supported by a Diagnostics Grant from the Dutch Digestive Foundation (D16-14). A.Z. holds a Rosalind Franklin fellowship from the University of Groningen. Sequencing of the control cohort was funded by a grant from the Netherlands’ Top Institute Food and Nutrition GH001 to C.W., who is further supported by an ERC advanced grant (ERC-671274) and a Spinoza award (NWO SPI 92-266). A.Z. is supported by an ERC starting grant (ERC-715772). J.F. and A.Z. are supported by a CardioVasculair Onderzoek Nederland grant (CVON 2012-03). Z.M. holds a Niels Stensen fellowship (from Amsterdam, the Netherlands).
Publisher Copyright:
© 2020, The Author(s).
PY - 2020/1/17
Y1 - 2020/1/17
N2 - 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. Here, via a metagenomics analysis of population-based and disease cohorts, Vich Vila et al. study the impact of 41 commonly used medications on the taxonomic structures, metabolic potential and resistome of the gut microbiome, underscoring the importance of correcting for multiple drug use in microbiome studies.
AB - 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. Here, via a metagenomics analysis of population-based and disease cohorts, Vich Vila et al. study the impact of 41 commonly used medications on the taxonomic structures, metabolic potential and resistome of the gut microbiome, underscoring the importance of correcting for multiple drug use in microbiome studies.
KW - arthritis
KW - identification
KW - irritable-bowel-syndrome
KW - proton pump inhibitors
KW - resistance
KW - RESISTANCE
KW - PROTON PUMP INHIBITORS
KW - IDENTIFICATION
KW - ARTHRITIS
KW - IRRITABLE-BOWEL-SYNDROME
U2 - 10.1038/s41467-019-14177-z
DO - 10.1038/s41467-019-14177-z
M3 - Article
C2 - 31953381
SN - 2041-1723
VL - 11
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 362
ER -