Proton-pump inhibitors increase <i>C. difficile</i> infection risk by altering pH rather than by affecting the gut microbiome based on a bioreactor model

<i>Clostridioides difficile</i> infections often occur after antibiotic use, but they have also been linked to proton-pump inhibitor (PPI) therapy. The underlying mechanism - whether infection risk is due to a direct effect of PPIs on the gut microbiome or changes in gastrointestinal pH - has remained unclear. To disentangle both possibilities, we studied the impact of the proton-pump inhibitor omeprazole and pH changes on key members of the human gut microbiome and stool-derived microbial communities from different donors <i>in vitro</i>. We then developed a custom multiple-bioreactor system to grow a model human microbiome community and a stool-derived community in chemostat mode and tested the effects of omeprazole exposure, pH changes, and their combination on <i>C. difficile</i> growth within these communities. Our findings show that changes in pH significantly affect the gut microbial community's biomass and the abundances of different bacterial taxa, leading to increased <i>C. difficile</i> growth within the community. However, omeprazole treatment alone did not result in such effects. These findings imply that the higher risk of <i>C. difficile</i> infection following proton-pump inhibitor therapy is probably because of alterations in gastrointestinal pH rather than a direct interaction between the drug and the microbiome. This understanding offers a new perspective on infection risks in proton-pump inhibitor therapy.