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The hidden dangers of proton pump inhibitors

  • Introduction

  • What are PPIs?

  • Use of Proton pump Inhibitors

  • Side effects

  • FAQs

Are Proton Pump Inhibitors the best way to treat heartburn and indigestion?

Well, if you have been popping PPIs every time you have a heart burn or indigestion, it's time to look into what it is doing to your body! Proton pump inhibitors are a class of medications commonly prescribed to reduce stomach acid production. They are used to treat various conditions such as GERD, peptic ulcers etc. While PPIs may give some symptomatic relief, they do come with some potential risks and side effects.

What are Proton Pump Inhibitors ?

Proton pump inhibitors are a class of medication which work by interfering with a system known as the “proton pump” in the cells of the stomach lining; actively reducing acid production.They inhibit the H+/K+-ATPase (proton pump) in parietal cells of the stomach.

Here are five most popular PPIs-






Use of Proton Pump Inhibitors

PPIs are used to treat stomach acid related symptoms.Some conditions in which PPIs are commonly given are-

  • Gastroesophageal disease (GERD)

  • Peptic ulcers

  • Helicobacter pylori infections

  • Heartburn

  • Zollinger-Ellison syndrome

  • Stomach cancer

Common side effects of Proton Pump Inhibitors:

Here are some of the main dangers associated with the long term use of PPIs:

1. PPIs increase risk of infection:

Stomach acid plays a crucial; role in killing bacteria that we may ingest with our food. By reducing stomach acid production, PPIs may increase the risk of certain infections, particularly gastrointestinal infections like Clostridium difficile (C. difficile) and community acquired pneumonia.Microbes that would ordinarily be killed in an acidic environment are able to travel unharmed into the small and large intestines when the pH of the stomach becomes basic.

2. PPIs may worsen SIBO:

PPI use may exacerbate SIBO because the chyme from the stomach that enters the small intestine's ability to maintain low bacterial populations depends on its acidity. When the researchers solely took into account studies that compared the incidence of SIBO before and after PPI use, they found a significant increase in SIBO. It's likely that SIBO induces reflux, which increases the need for PPIs, which in turn causes PPIs to reduce stomach acid and exacerbate SIBO.

3. PPIs can cause Nutritional deficiencies:

Stomach acid helps with the absorption of certain nutrients such as vitamin B12, magnesium, calcium, and iron. Long-term PPI use can potentially lead to deficiencies in these essential nutrients, which may cause various health issues, including anaemia bone problems.

4. PPIs increase fracture risk:

Some studies suggested that long term PPI use may be associated with a higher risk of fractures, especially in older adults. This risk may be related to potential nutrient deficiencies and impaired calcium absorption due to reduced stomach acid.

5. PPIs can cause Kidney damage:

In rare cases, long term PPI use has been associated with acute interstitial nephritis, a type of kidney inflammation that can potentially lead to kidney damage if not promptly diagnosed and treated.

6. PPIs exacerbate liver disease by altering the microbiota:

Three different kinds of chronic liver disease, including alcohol-induced liver disease, non-alcoholic steatohepatitis, and NAFLD, can be aggravated by Enterococcus bacteria that proliferate when PPIs are used. These bacteria can cause inflammation when translocated to the liver.

7. PPIs increase risk of iron deficiency anaemia:

A 2.49 times greater risk of developing iron insufficiency was linked to PPI use. The connection diminished after acid-suppressing medication was stopped, and it was significantly stronger for individuals who took large daily doses.Iron-insufficiency anaemia can result from prolonged iron deficiency.

Root cause approach to treat heartburn and indigestion

1. Low carb diet: Diet rich in carbohydrates can cause inflammation of the stomach. Switch to a low carbohydrate diet.

2. Treat nutrient deficiencies : For example iodine and choline are responsible for production and secretion of stomach acid. Zinc is used by the stomach to produce HCl.

3. Treat SIBO:Lower esophageal sphincter dysfunction, which permits stomach contents to reflux back into the oesophagus, is thought to be mostly caused by intra-abdominal pressure from SIBO. By treating SIBO, this pressure can be released, and the frequency and intensity of heartburn are frequently markedly diminished.

4. Replace stomach acid: The majority of GERD patients suffer from too little rather than too much stomach acid. Zinc is used by the stomach to produce HCl. Betaine hcl is also found to be useful

5. Take probiotics: Probiotics help to increase good gut microbiome.

Before stopping the usage of PPIs, always talk to your doctor and make sure to go off the medication gradually to prevent any withdrawal symptoms.


It is crucial to use PPIs judiciously and under the guidance of a healthcare professional. Long term PPI have been associated with many chronic diseases like autoimmune conditions, Obesity, Metabolic dysfunction, etc. If you have been on PPIs for a long time,work with a Functional Medicine Practitioner to help you wean off the PPIs by addressing the root cause of GERD or chronic heartburn. With right lifestyle changes, food and certain nutraceuticals, you can regain your gut health.


1. Are proton pump inhibitors safe to use?

When used as prescribed and for short-term treatment, PPIs are generally safe for most people. However, long-term use carries potential risks and side effects.

2. Can PPIs lead to nutritional deficiencies?

Long term PPI use may lead to deficiencies in essential nutrients like vitamin B12, magnesium, calcium, and iron, which can cause health issues like anaemia and bone problems. Stomach acid is needed for protein break down. So long term PPIs can cause low protein as well.

3. How can I minimise the risks associated with PPI use?

To minimise risks, use PPIs as prescribed and only for the recommended duration. If you have been on PPIs for a long time, work with a Functional Medicine Practitioner to help you wean off

4. Are PPIs safe to take with other medications?

By decreasing their absorption from the stomach, PPIs may reduce the effectiveness of various drugs. Before combining these medications with other prescription medications, make sure you carefully read the product box and speak with your pharmacist.

5. Should I stop taking my PPI medication?

Do not stop taking your PPI without consulting your healthcare provider. Abruptly stopping PPIs can lead to rebound symptoms and may not be safe for your condition. Always seek guidance from a medical professional before making any changes to your medication regimen.


  • Heidelbaugh JJ, Goldberg KL, Inadomi JM. Adverse Risks Associated With Proton Pump Inhibitors: A Systematic Review. Gastroenterol Hepatol (N Y). 2009 Oct;5(10):725–34. PMCID: PMC2886361.

  • Li T, Xie Y, Al-Aly Z. The association of proton pump inhibitors and chronic kidney disease: cause or confounding?Curr Opin Nephrol Hypertens. 2018 May;27(3):182-187. doi: 10.1097/MNH.0000000000000406. PMID: 29432214.

  • Johnstone J, Nerenberg K, Loeb M. Meta-analysis: proton pump inhibitor use and the risk of community-acquired pneumonia. Aliment Pharmacol Ther. 2010;31(11):1165-1177.

  • Fujimori S. What are the effects of proton pump inhibitors on the small intestine? World J Gastroenterol. 2015 Jun 14;21(22):6817-9. doi: 10.3748/wjg.v21.i22.6817. PMID: 26078557; PMCID: PMC4462721.

  • Al-Hadrawy SMJ, Mahdi Al-Turfi ZS. Effects of the Long-term Treatment of Proton Pump Inhibitors on the Function of Kidney and Liver in Laboratory Female Rats. Arch Razi Inst. 2021 Oct 31;76(4):975-983. doi: 10.22092/ari.2021.355947.1745. PMID: 35096333; PMCID: PMC8791006.

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