PPI Intake and Gut Health: What are the Impacts?

August 4, 2021 ,

What are PPIs?

Proton Pump Inhibitors (PPIs) – esomeprazole, lansoprazole, omeprazole, pantoprazole and rabeprazole – are among the most widely used drugs in the world. They allow for the management of gastric acidity for gastric ulcers, duodenal ulcers, or gastroesophageal reflux disease (GERD).

What do they do?

As the name suggests, PPIs inhibit the proton pump, an active membrane carrier, which moves protons (H+ ions) from outside the gastric cell to the inside. This reduces the pH (acidification) of the parietal gastric cells responsible for producing the hydrochloric acid necessary for good digestion.

Taking PPIs, by inhibiting the activity of the proton pump, inhibits the secretion of gastric acid by the cells of the stomach, which helps relieve pain, burning sensations, or discomfort in the abdomen.

Does taking them induce side effects?

Like any medication, taking PPIs can cause adverse effects. Among the most common are abdominal pain, diarrhea, constipation, nausea, and headaches.

Although these medications are safe, some studies question the negative long-term impacts of their use. In effect, prolonged use could lead to a greater risk of fractures, pneumonia, vitamin B12 deficiency, kidney disease and dementia. However, current data is not sufficient to establish a direct causal link between these serious adverse reactions and long-term PPI intake.

On the other hand, it is recognized that the use of PPIs is associated with an increased risk of enteric infections by toxic bacteria such as E. coli, Salmonella, and Clostridium difficile. This could be explained by the alteration of the intestinal microbiota which creates intestinal dysbiosis.

This raises the issue of the impact of PPI medications on the intestinal microbiota.

What are the effects on the gut microbiota?

More and more studies are looking at the pivotal role of the intestinal microbiota and the impact of its alteration on our health, in particular on gastrointestinal disorders.

Taking antibiotics is known to alter the gut microbiota, but what about taking PPIs?

Several studies and literature reviews point to the fact that taking PPIs can alter the intestinal microbiota, more or less markedly, in all parts of the gastrointestinal tract. This alteration would begin in the esophagus, continue into the stomach, then in the small intestine and finally into the colon. Taking PPIs could therefore affect bacterial diversity and induce profound changes in the intestinal microbiota.

Among the changes observed is the overrepresentation of oral microbiota in the gut microbiota of PPI users. This supports the fact that the inhibition of gastric acid secretion induced by PPIs facilitates the colonization of the distal parts of the digestive tract by pathogenic or non-pathogenic microbial species in the upper gastrointestinal microbiota.

It should also be noted that an imbalance between the bacteria that make up the intestinal microbiota can promote the inflammation of the intestinal epithelium. This is often the case in people with inflammatory bowel disease (IBD). It is therefore questionable whether there is an exact link between taking PPIs and the increasing incidence of IBD and other gastrointestinal disorders.

Taking PPIs and SIBO

Several studies published in recent years suggest that in addition to affecting the gut microbiota and increasing the risks associated with enteric infections, taking PPIs could also increase the risks of bacterial overgrowth of the small intestine (SIBO).

However, this association is controversial due to the conflicting results of studies conducted to date. A 2018 meta-analysis reported that PPI treatment was associated with a moderately increased risk of SIBO, while other studies found no difference between PPI users compared to non-users.

In conclusion

Although more studies are needed to measure the exact impact of taking PPIs on gut health, and the resulting consequences for human health, it is prudent to remain vigilant, knowing that they are among the most widely used medicines. They should only be taken with the supervision of your doctor, while also knowing that depending on the person and the situation, other alternatives can be considered to relieve discomfort, such as better eating habits.

Our meal plan for gastroesophageal reflux, which is customizable according to your allergies, intolerances and preferences, could very well help you. To guide you towards the approach that will best suit your needs, we also offer consultations with a dietitian who specializes in gastrointestinal health.



Nehra, A. K., Alexander, J. A., Loftus, C. G., & Nehra, V. (2018, February). Proton pump inhibitors: review of emerging concerns. In Mayo Clinic Proceedings (Vol. 93, No. 2, pp. 240-246). Elsevier.

Imhann, F., Bonder, M. J., Vila, A. V., Fu, J., Mujagic, Z., Vork, L., … & Zhernakova, A. (2016). Proton pump inhibitors affect the gut microbiome. Gut, 65(5), 740-748.

Société canadienne de recherche intestinale. 2016. « Les IPP font-ils obstacle au microbiome intestinal? https://badgut.org/centre-information/sujets-de-a-a-z/les-ipp-font-ils-obstacle-au-microbiome-intestinal/?lang=fr [accessed July 27, 2021].

Imhann, F., Vich Vila, A., Bonder, M. J., Lopez Manosalva, A. G., Koonen, D. P., Fu, J., … & Weersma, R. K. (2017). The influence of proton pump inhibitors and other commonly used medication on the gut microbiota. Gut microbes, 8(4), 351-358.

Bruno, G., Zaccari, P., Rocco, G., Scalese, G., Panetta, C., Porowska, B., … & Severi, C. (2019). Proton pump inhibitors and dysbiosis: Current knowledge and aspects to be clarified. World journal of gastroenterology, 25(22), 2706.

Macke, L., Schulz, C., Koletzko, L., & Malfertheiner, P. (2020). Systematic review: the effects of proton pump inhibitors on the microbiome of the digestive tract—evidence from next‐generation sequencing studies. Alimentary pharmacology & therapeutics, 51(5), 505-526.

Su, T., Lai, S., Lee, A., He, X., & Chen, S. (2018). Meta-analysis: proton pump inhibitors moderately increase the risk of small intestinal bacterial overgrowth. Journal of gastroenterology, 53(1), 27-36.Shah, A., Talley, N. J., Jones, M., Kendall, B. J.,

Koloski, N., Walker, M. M., … & Holtmann, G. J. (2020). Small intestinal bacterial overgrowth in irritable bowel syndrome: a systematic review and meta-analysis of case-control studies. Official journal of the American College of Gastroenterology| ACG, 115(2), 190-201.

Weitsman, S., Celly, S., Leite, G., Mathur, R., Sedighi, R., Barlow, G. M., … & Pimentel, M. (2021). Effects of Proton Pump Inhibitors on the Small Bowel and Stool Microbiomes. Digestive Diseases and Sciences, 1-9.


Jennifer Morzier
Jennifer is a Registered Dietitian graduated from the University of Montreal in December 2018 and is a member of the Ordre professionnel des diététistes du Québec (OPDQ). She believes that the quality of our food choices has a direct impact on our health and energy level. Her goal? To help people improve the quality of what they put in their plates, for their better well-being and greater pleasure.

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