Gut microbiota & Proton Pump Inhibitors (PPIs)

Proton Pump Inhibitors (PPIs) may alter the relative prevalence of certain organisms in the lower esophagus while having a lesser effect on the proximal esophagus. Changes in the esophageal microbiome have been correlated with some esophageal diseases.
Bilello & Okereke 2021 Biomedicines 9: 617

Proton Pump inhibitors cause alterations in the composition of both the upper and distal gut microbiota. However, the functional relevance of Proton Pump inhibitors-induced dysbiosis remains unclear. The involvement of gut microbiota in PPI-associated adverse events is still largely inconclusive.
Macke et al. 2020a Aliment Pharmacol Ther 51(5): 505-526

In fecal samples, Proton Pump Inhibitors (PPIs) have been observed to increase multiple taxa from various orders and families:

Orders:

• Bacillales (e.g.,Staphylococcaceae)


• Lactobacillales (e.g.,Enterococcaceae, Lactobacillaceae, Streptococcaceae)


• Actinomycetales (e.g., Actinomycetaceae, Micrococcaceae)

Families:

• Pasteurellaceae


• Enterobacteriaceae

Genus:

• Veillonella

Conversely, Proton Pump inhibitors have been found to decrease the presence of certain taxa, including:

Class:

• Mollicutes

Families:

• Bifidobacteriaceae


• Ruminococcaceae


• Lachnospiraceae

These findings are based on fecal samples from 19 independent cohorts, comprising 790 Proton Pump inhibitors users.
Macke et al. 2020a Aliment Pharmacol Ther 51(5): 505-526

Proton Pump inhibitors are generally well tolerated but can increase the risk of an imbalance in gut microbiota composition (i.e., dysbiosis).
Bruno et al. 2019 World J Gastroenterol 25(22): 2706-2719

PPIs cause a bacterial imbalance, such as the reduction (↓) of Actinobacteria and Bifidobacteria spp., which is responsible for the mucosal damage. PPIs increase the expression of bacteria with beta-glucuronidases activity
Bruno et al. 2019 World J Gastroenterol 25(22): 2706-2719)

In the water avoidance stress treatment, PPI significantly enhanced intestinal permeability in vivo compared to that in vehicle treratment.
Takashima et al. 2020 Neurogastroenterology & Motility 32: e13841

PPI-treated FMT significantly increased the intestinal permeability in vivo compared to that in vehicle-treated FMT
Takashima et al. 2020 Neurogastroenterology & Motility 32: e13841

Proton pump inhibitors treatment altered the gut microbiota composition, indicating that PPI induced dysbiosis.
Takashima et al. 2020 Neurogastroenterology & Motility 32: e13841

The use of PPIs is generally well tolerated. However, their long-term use exposes patients to an increased risk of developing extra-intestinal disorders (Eom et al. 2011 CMAJ 183: 310-319; de la Coba Ortiz et al. 2016 Rev Esp Enferm Dig 108: 207-224; Islam et al. 2018 Eur J Gastroenterol Hepatol 30: 1395-1405), likely due to PPI-driven gastric hypochlorhydria , which can also cause significant changes in gut microbiota composition (Freedberg et al. 2015 Gastroenterology 149: 883-5; Tsuda et al. 2015 Clin Transl Gastroenterol 6: e89; Takagi et al. 2018 J Clin Biochem Nutr 62: 100-105)

see also:
Adverse Events / Safety & Proton Pump Inhibitors (PPIs)
Gut microbiota & Omeprazole