The impact of proton pump inhibitors on the human gastrointestinal microbiome

Clin Lab Med. 2014 Dec;34(4):771-85. doi: 10.1016/j.cll.2014.08.008. Epub 2014 Sep 24.


Potent gastric acid suppression using proton pump inhibitors (PPIs) is common in clinical practice but may have important effects on human health that are mediated through changes in the gastrointestinal microbiome. In the esophagus, PPIs change the normal bacterial milieu to decrease distal esophageal exposure to inflammatory gram-negative bacteria. In the stomach, PPIs alter the abundance and location of gastric Helicobacter pylori and other bacteria. In the small bowel, PPIs cause polymicrobial small bowel bacterial overgrowth and have been associated with the diagnosis of celiac disease. In the colon, PPIs associate with incident but not recurrent Clostridium difficile infection.

Keywords: Barrett's esophagus; Clostridium difficile infection; Gastric acid suppression; Helicobacter pylori; Human microbiome; Hypergastrinemia; Proton pump inhibitors; Small bowel bacterial overgrowth.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Celiac Disease / etiology*
  • Celiac Disease / microbiology
  • Gastrointestinal Tract / chemistry
  • Gastrointestinal Tract / drug effects
  • Gastrointestinal Tract / microbiology*
  • Humans
  • Hydrogen-Ion Concentration
  • Microbiota / drug effects*
  • Proton Pump Inhibitors / adverse effects*
  • Proton Pump Inhibitors / chemistry
  • Proton Pump Inhibitors / therapeutic use


  • Proton Pump Inhibitors