Publication

Proton pump inhibitors affect the gut microbiome

Imhann, F., Bonder, M. J., Vich Vila, A., Fu, J., Mujagic, Z., Vork, L., Feenstra, E. T., Jankipersadsing, S. A., Cenit, M. C., Harmsen, H. J. M., Dijkstra, G., Franke, L., Xavier, R. J., Jonkers, D., Wijmenga, C., Weersma, R. K. & Zhernakova, A., May-2016, In : Gut. 65, 5, p. 740-748 10 p.

Research output: Contribution to journalArticleAcademicpeer-review

BACKGROUND AND AIMS: 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 difficile. The gut microbiome plays an important role in enteric infections, by resisting or promoting colonisation by pathogens. In this study, we investigated the influence of PPI use on the gut microbiome.

METHODS: The gut microbiome composition of 1815 individuals, spanning three cohorts, was assessed by tag sequencing of the 16S rRNA gene. The difference in microbiota composition in PPI users versus non-users was analysed separately in each cohort, followed by a meta-analysis.

RESULTS: 211 of the participants were using PPIs at the moment of stool sampling. PPI use is associated with a significant decrease in Shannon's diversity and with changes in 20% of the bacterial taxa (false discovery rate <0.05). Multiple oral bacteria were over-represented in the faecal microbiome of PPI-users, including the genus Rothia (p=9.8×10(-38)). In PPI users we observed a significant increase in bacteria: genera Enterococcus, Streptococcus, Staphylococcus and the potentially pathogenic species Escherichia coli.

CONCLUSIONS: The differences between PPI users and non-users observed in this study are consistently associated with changes towards a less healthy gut microbiome. These differences are in line with known changes that predispose to C. difficile infections and can potentially explain the increased risk of enteric infections in PPI users. On a population level, the effects of PPI are more prominent than the effects of antibiotics or other commonly used drugs.

Original languageEnglish
Pages (from-to)740-748
Number of pages10
JournalGut
Volume65
Issue number5
Publication statusPublished - May-2016

    Keywords

  • CLOSTRIDIUM-DIFFICILE INFECTION, INTESTINAL MICROBIOTA, RESISTANCE, DIARRHEA, COLONIZATION, PATHOGENS, DYSBIOSIS, BACTERIA, THERAPY, OBESITY

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