Proton pump inhibitors affect the gut microbiome

By F. Imhann, M. Bonder, A. Vich Vila, Jingyuan Fu, Z. Mujagic, L. Vork, E. Tigchelaar, S. Jankipersadsing, M. Cenit, H. Harmsen and 7 more. Gut, 2015

1,218 citations recorded by the source corpus.

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.

Subfields: Food Science, Infectious Diseases, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b8fb7b6609e0c21615cf6b305fc4c0b643f9fe55

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Citations in the corpus

Gut Microbiome: Profound Implications for Diet and Disease (2019, background): “Antibiotics, PPIs, and atypical antipsychotics have each been implicated in reducing alpha microbial diversity [286,290,291].”
Human gut microbiome: hopes, threats and promises (2018, background): “118 122 Thus, one may argue that we should take into account of such confounding factor for all the future studies, including neurodegenerative disorders.”
Extensive impact of non-antibiotic drugs on human gut bacteria (2018, neutral): “When we probed for higher, more physiological intestinal metformin concentrations, 3 of 22 tested strains were inhibited at concentrations below 1.5 mM (ED Fig.”
Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights (2016, background): “The influence of confounding factors on human microbiome has been scarcely investigated in the literature [54, 55], but recent studies [44, 45] highlight this problem and question the study design of some works.”
The Human Gut Microbiome: From Association to Modulation. (2018, neutral): “Similarly, proton pump 177 inhibitors (Freedberg et al., 2015; Imhann et al., 2016; Jackson et al., 2016), atypical 178 antipsychotics (Bahr et al., 2015; Flowers et al., 2017; Mäkivuokko et al., 2010) and non-179 steroidal anti-inflammatory drugs (Rogers and Aronoff, 2016), among others, have been…”
The gut microbiome: Relationships with disease and opportunities for therapy (2018, background): “, 2016), pharmaceuticals such as proton pump inhibitors (Imhann et al., 2016), xenobiotics (Maurice et al.”