We read with great interest the recent publications in Gut by Imhann et al and Jackson et al, which assessed the impact of proton pump inhibitor (PPI) use on gut microbiota diversity and composition in humans. 1 2 PPIs are one of the most commonly used drug classes worldwide. Once initiated, they are often used chronically without clear therapeutic intent. 3 PPIs alter GI pH4 and delay gastric emptying rate, 5 which could directly affect gut microbiota and survival of enteric pathogens. Using three independent cohorts (211 PPI users and 1604 non-users), Imhann et al1 reported a significant decrease in alpha diversity and changes in 20% of bacterial taxa in PPI users compared with non-users.

Among 1827 healthy twins, Jackson et al2 also found a significant decrease in alpha diversity and alteration of bacterial composition in PPI users. Notably, both studies found a higher abundance of oral commensals, including Streptococcaceae, among PPI users. These studies controlled for some potential confounders in their analyses; however, intersubject variability could have influenced their results. We assessed the impact of PPI use on the gut microbiota composition in a prospective study of healthy older adults (age≥ 60 years) from San Antonio, Texas, USA. Participants provided a stool sample at baseline, completed a 14-day course of omeprazole 20 mg daily and then provided a follow-up stool sample. Stool 16 s rRNA V4 sequences were amplified and sequenced on the Illumina MiSeq platform. Sequences were clustered into operational taxonomic units (OTUs) and classified via mothur’s Bayesian classifier referenced against the Greengenes database. Abundance-weighted sample differences were calculated using the Bray-Curtis dissimilarity. PERMANOVA was used to assess the impact of PPI use on beta diversity.