The Influence of Oral Proton Pump Inhibitors on the Fecal Microbiome of Infants with Gastroesophageal Reflux

Background: The aim of this study was to determine the effect of oral PPIs on the fecal microbiome in infants with gastroesophageal reflux disease (GERD).Methods: In this prospective longitudinal study 12 infants with proven GERD received oral PPIs for a mean period of 18 weeks (range 8-44). Stool samples were collected before (“before PPI”) and 4 weeks after initiation of PPI therapy (“on PPI”). A third sample was obtained 4 weeks after PPI discontinuation (“after PPI”). The fecal microbiome was determined by NGS based 16S rDNA sequencing. To address possible confounders the correlation between microbiome and patients´ age/nutrition was calculated.Results: In a comparison of “before PPI” and “on PPI” neither α- nor β-diversity changed significantly. The relative abundances showed a decrease of unclassified Lactobacillales and Xanthomonadales and an increase of Pasteurellales. After PPI therapy there was a significant increase of α- and β-diversity. Additionally, the relative abundances of the phyla Firmicutes, Bacteroidetes and Proteobacteria were significantly changed and correlated to patients´ age and the introduction of solid foods.Conclusions: PPI treatment has only minor effects on the fecal microbiome. After discontinuation of PPI treatment the fecal microbiome correlated to patients´ age and nutrition.