This study investigates the impact of proton pump inhibitors (PPIs) on the gut microbiome. PPIs are among the top 10 most widely used drugs globally, and their use has been associated with an increased risk of enteric infections, particularly *Clostridium difficile*. The gut microbiome plays a crucial role in resisting or promoting the colonization of pathogens. The study analyzed the gut microbiome composition of 1815 individuals from three cohorts using tag sequencing of the 16S rRNA gene. PPI use was found to significantly decrease Shannon's diversity and alter the composition of 20% of bacterial taxa. PPI users showed a significant increase in oral bacteria and potentially pathogenic bacteria, such as *Enterococcus*, *Streptococcus*, *Staphylococcus*, and *Escherichia coli*. These changes are consistent with known alterations 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 PPIs on the gut microbiome are more pronounced than those of antibiotics or other commonly used drugs. The findings highlight the need for healthcare practitioners and researchers to consider the influence of PPIs on the gut microbiome, especially given the widespread use of PPIs and the increasing number of studies investigating the microbiome.This study investigates the impact of proton pump inhibitors (PPIs) on the gut microbiome. PPIs are among the top 10 most widely used drugs globally, and their use has been associated with an increased risk of enteric infections, particularly *Clostridium difficile*. The gut microbiome plays a crucial role in resisting or promoting the colonization of pathogens. The study analyzed the gut microbiome composition of 1815 individuals from three cohorts using tag sequencing of the 16S rRNA gene. PPI use was found to significantly decrease Shannon's diversity and alter the composition of 20% of bacterial taxa. PPI users showed a significant increase in oral bacteria and potentially pathogenic bacteria, such as *Enterococcus*, *Streptococcus*, *Staphylococcus*, and *Escherichia coli*. These changes are consistent with known alterations 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 PPIs on the gut microbiome are more pronounced than those of antibiotics or other commonly used drugs. The findings highlight the need for healthcare practitioners and researchers to consider the influence of PPIs on the gut microbiome, especially given the widespread use of PPIs and the increasing number of studies investigating the microbiome.