The Gastric and Intestinal Microbiome: Role of Proton Pump Inhibitors

Curr Gastroenterol Rep. 2017 Aug;19(8):42. doi: 10.1007/s11894-017-0577-6.


Purpose of review: The discovery of Helicobacter pylori and other organisms colonizing the stomach and the intestines has shed some light on the importance of microbiome in maintaining overall health and developing pathological conditions when alterations in biodiversity are present. The gastric acidity plays a crucial role in filtering out bacteria and preventing development of enteric infections. In this article, we discuss the physiology of gastric acid secretion and bacterial contribution to the composition of gastric and intestinal barriers and review the current literature on the role of proton pump inhibitors (PPIs) in the microbial biodiversity of the gastrointestinal tract.

Recent findings: Culture-independent techniques, such as 16S rRNA sequencing, have revolutionized our understanding of the microbial biodiversity in the gastrointestinal tract. Luminal and mucosa-associated microbial populations are not identical. Streptococcus is overrepresented in the biopsies of patients with antral gastritis and may also be responsible for the development of peptic ulcer disease. The use of PPIs favors relative streptococcal abundance irrespective of H. pylori status and may explain the persistence of dyspeptic symptoms in patients on PPI therapy. Increased risk of enteric infections has also been seen in patients taking PPIs. The overuse of PPIs leads to significant shift of the gastrointestinal microbiome towards a less healthy state. With the advent of PPIs, many studies have demonstrated the significant changes in the microbial composition of both gastric and intestinal microbiota. Although they are considered relatively safe over-the-counter medications, PPIs in many cases are over- and even inappropriately used. Future studies assessing the safety of PPIs and their role in the development of microbiome changes should be encouraged.

Keywords: Gastrointestinal tract; Helicobacter pylori; Microbiome; Microbiota; Proton pump inhibitors (PPIs).

Publication types

  • Review

MeSH terms

  • Gastric Acid / metabolism*
  • Gastritis / microbiology
  • Gastrointestinal Microbiome / drug effects*
  • Helicobacter pylori
  • Humans
  • Peptic Ulcer / microbiology
  • Proton Pump Inhibitors / adverse effects*
  • RNA, Ribosomal, 16S / genetics
  • Streptococcus / pathogenicity


  • Proton Pump Inhibitors
  • RNA, Ribosomal, 16S