Peptic ulcers, gastroesophageal reflux, and other gastrointestinal disorders are often treated with proton pump inhibitors (PPIs). So far, the effects of this widely prescribed medication on gut microbiota have not been investigated in a large cohort.

In a recent Gut paper, Jackson, et al. investigated the association between PPI use and gut microbiota composition. They examined the fecal samples of 1827 healthy twins from the TwinsUK cohort, and found lower microbial diversity and decreased abundance of gut commensals in PPI users (independent of antibiotic use). The gut microbiota of individuals who used PPIs showed a higher abundance of bacteria from the oral and upper gastrointestinal tract — in particular, a significant increase in Streptococcaceae. The researchers replicated these main findings in a small interventional study of 70 identical twin pairs who were discordant for PPI use.

Authors hypothesize that the observed microbiome changes are attributable to PPIs’ removal of the low pH ‘barrier’ between the upper and lower gastrointestinal tract. They say their data show a possible downside of PPI administration, and thus, should motivate caution against over-prescribing PPIs. They do not yet know if the observed gut microbiota shifts account for the increased risk of enteric infections in PPI users.


Jackson MA, et al. (2015) Proton pump inhibitors alter the composition of the gut microbiota. Gut doi:10.1136/gutjnl-2015-310861