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Proton pump inhibitors affect the gut microbiome.

Floris Imhann1, Marc Jan Bonder2, Arnau Vich Vila1

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Proton pump inhibitor (PPI) use significantly alters the gut microbiome, decreasing diversity and increasing potentially harmful bacteria. These changes may explain the higher risk of enteric infections in PPI users.

Keywords:
ENTERIC INFECTIONSINTESTINAL BACTERIAPROTON PUMP INHIBITION

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Area of Science:

  • Microbiology
  • Gastroenterology
  • Pharmacology

Background:

  • Proton pump inhibitors (PPIs) are widely used globally.
  • PPI use is linked to an increased risk of enteric infections, particularly Clostridium difficile.
  • The gut microbiome is crucial in modulating pathogen colonization.

Purpose of the Study:

  • To investigate the impact of PPI usage on the composition of the human gut microbiome.
  • To determine if PPI-induced microbiome changes correlate with increased susceptibility to enteric infections.

Main Methods:

  • Analysis of gut microbiome composition in 1815 individuals across three cohorts using 16S rRNA gene sequencing.
  • Comparison of microbiota composition between PPI users and non-users within each cohort.
  • Meta-analysis to consolidate findings from the individual cohorts.

Main Results:

  • PPI use was associated with a significant reduction in gut microbial diversity (Shannon's diversity).
  • Significant alterations were observed in 20% of bacterial taxa in PPI users.
  • Over-representation of oral bacteria (e.g., Rothia) and an increase in potentially pathogenic bacteria (e.g., Enterococcus, Streptococcus, Staphylococcus, Escherichia coli) were noted in PPI users.

Conclusions:

  • PPI use leads to gut microbiome changes indicative of a less healthy state.
  • These microbiome alterations align with known risk factors for Clostridium difficile infections.
  • The impact of PPIs on the gut microbiome is more pronounced than that of antibiotics or other common medications at a population level.