PPI Side Effects: Loss of Essential Nutrients & More | Sepalika
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Acid Reflux

How Proton Pump Inhibitors (PPIs) Are Robbing Nutrients from Your Body

Jun 27, 2017

Bob was a social animal. He loved meeting people and more often than not, was the live wire at parties and get-togethers. At night, in the silence of the after-party when he would go home to call it a day, it would come. The dreaded heartburn. The hot bile would rise up his throat, threatening to spill all the fun of the evening as if chastising him for being a bit too wild. Bob would rush to the bathroom and gulp a couple of pills. They were Proton Pump Inhibitors, the technical name given to designer antacids. Within minutes, relief would come, and he would collapse on his bed.

Bob had been taking acid-blockers, or more specifically Proton Pump Inhibitors, for his acid reflux for a year and a half. After over the counter antacids did nothing for him, he talked to his doctor, who prescribed PPIs. They worked immediately, and he had continued to use them since then.

The Dark Side of PPIs: They Steal Nutrients From Your Body

Of late, Bob had been feeling tremors. He put it down to partying too hard and carried on. One day at a friend’s house, the tremors felt more severely. Attributing them to the couple of beers he just had, he dismissed them and went about doing what he did best – entertaining his friends with his stories. And then suddenly he had a seizure. He started trembling violently and collapsed on the floor. There was panic and hysteria in the room. Someone dialed 911. Within 20 minutes, he was at the nearest hospital.

So what went wrong? Bob was diagnosed with severe hypomagnesia. The doctors had a hard time controlling his severe loss of magnesium, which had also caused deficiencies of calcium and potassium. It also led to metabolic acidosis, a condition in which his body was producing far more acid than was required and his kidneys were unable to remove the excess acid from the body. While in the hospital, Bob contracted a pneumonia infection as well. When doctors tried to piece the story together, they found the culprit – the various “prazoles” Bob had been taking for relieving his acidity. Bob was unlucky to be among those who experience such severe repercussions from overuse of PPIs. Bob’s condition is an example of how many things can go wrong with a person due to PPI side effects.

What Are Proton Pump Inhibitors (PPIs)?

Proton pump inhibitors are a class of drugs that inhibit acid production in the stomach. They are prescribed to people who suffer from acidity (or acid reflux or heartburn). Bob is among the 15 million Americans who use PPI medication for dealing with their acid reflux. And while PPIs are regularly recommended for relieving acid reflux, the increased health risks of PPI overuse cannot be ignored.

Commonly Prescribed PPIs

The names of PPI drugs usually end with “-prazole”

  • omeprazole (Prilosec, Prilosec OTC)
  • lansoprazole (Prevacid, Prevacid IV, Prevacid 24-Hour)
  • dexlansoprazole (Dexilent, Dexilent Solutab)
  • rabeprazole (Aciphex, Aciphex Sprinkle)
  • pantoprazole (Protonix)
  • esomeprazole (Nexium, Nexium IV, Nexium 24 HR)

Vimovo is a combination of esomeprazole magnesium/naproxen, Yosprala is a combination of aspirin and omeprazole, while Zegerid and Zegerid OTC is a combination of omeprazole and sodium bicarbonate.

How Do PPIs Work In Our Body?

Special cells in the stomach, called parietal cells, produce and secrete acid into the stomach. Acid is required to digest food properly. It activates various enzymes that break down complex food particles into simple, absorbable units. Proton pump inhibitors, as the name suggests, inhibit an enzyme system which is meant to ‘pump’ the acid into the stomach. Less acid equals immediate relief from heartburn, which is why PPIs are effective most of the times.

Side Effects That Could Happen Soon After You Start Taking PPIs

A study reported in the journal Alzheimer’s Research and Therapy found that healthy volunteers showed a marked deterioration in cognitive functions after just one week of consuming different PPIs. Another study had previously found that use of lansoprazole enhances production of something called as amyloid beta plaque. Deposits of Amyloid beta plaque cause neurocognitive diseases such as dementia and Alzheimer’s. The former study extends this finding to all the major classes of proton pump inhibitors. The study shows that the use of any PPI is capable of deteriorating mental function and can lead to Alzheimer’s disease in the future.

Another side effect that could happen soon after you start PPI treatment is Clostridium difficle infection. The risk of this infection increases dramatically, within just a couple of days of starting to use PPI’s. Cl. difficle is a bacterium that causes diarrhea and a more serious digestive condition called colitis, or inflammation of the colon. Symptoms like watery stools, fever, loss of appetite, nausea and abdominal tenderness and pain are common in this type of infection.

Use of PPI drugs is also linked to a greater risk of community-acquired pneumonia. Patients who have been hospitalized and use breathing devices are at a greater risk of this type of infection.

Nutrient Depletion From Using PPIs Over The Long Term

PPI Side effects

PPI Side effects

A study on more than 73,000 people (age 75 and more) found that those using PPIs regularly had a 44% increased risk of developing dementia than non-users.

The majority of problems caused by long-term use of PPIs are due to nutrient depletion. Most people are surprised to learn that PPIs interfere with the absorption of certain nutrients that we are supposed to get from our food. Subsequently, this depletion leads to serious health consequences.


What Bob suffered from was a case of severe magnesium depletion that caused further side effects. Long-term PPI medication use is associated with the risk of hypomagnesia, which is a serious condition. Research shows that of the people who suffered from hypomagnesia, nearly 25% had a persistent condition that couldn’t be corrected even with proper supplementation. Magnesium plays a vital role in our health. And when the body is in a state of magnesium deficiency, it can lead to a host of serious health complications.


Calcium is absorbed only in the presence of high-quality stomach acid. So any drug that interferes with acid production also makes it harder for the body to absorb calcium effectively. We know the importance of calcium not just in bone health but also in cardiac health. In fact, calcium is vital for functions like muscle contraction and protein regulation. A calcium deficient condition will severely hamper all of these activities.


Zinc is essential in various important bodily functions such as immune response, night vision, new bone formation, tissue growth and ensuring the stability of cell membranes. It has been shown that zinc absorption is severely hampered when the stomach acid pH goes above 5 (more alkaline, less acidic). When PPIs suppress acid production, pH levels naturally rise. As a result, zinc absorption does not happen effectively.

Vitamin B12

Low gastric acidity also hampers vitamin B12 absorption from dietary proteins. In individuals taking PPI medication over the long term, supplementation of B12 is required to correct this deficiency. A study showed that individuals on PPIs had 70 to 90% reduced B12 absorption.


Folate absorption is reduced drastically in the presence of low stomach acid. According to a study published in the Journal of Laboratory and Clinical Medicine, use of PPIs hampered folate absorption.


A study showed that iron absorption was hampered in 80% of the participants due to reduced stomach acidity. Iron deficiency causes anemia. It is a condition where the body does not get enough iron to produce hemoglobin, the protein in RBCs which supplies oxygen to every cell in the body. A lack of oxygen can make the cells starve.

Long-term Use Of PPIs  Can Increase Risk of Infections

  • Clostridium difficle
  • Traveler’s Diarrhea
  • Pneumonia
  • Small intestinal bacterial overgrowth (SIBO)
  • Spontaneous bacterial peritonitis (inflammation of the peritoneum due to bacterial infection; peritoneum is the thin layer of tissue that covers the inside of the abdomen as well the major organs) and
  • Interstitial nephritis (swelling and inflammation in between kidney tubules)

PPIs May Impact Proton Pumps Everywhere In The Body

Proton pumps are the most common type of transporter gateway proteins present in almost all cells of the body. They perform a crucial role in energy production for various cells and organs. Proton pumps form the basis of aerobic respiration – a process where glucose is broken down in the absence of oxygen and energy is released. This energy is then used to produce ATP molecules – the energy currency of our body’s cells.

Without efficient proton pumps, our body will have to rely on the less effective anaerobic system of energy production. This will lead to rapid fatigue as anaerobic systems will not be able to cope with the body’s demand for energy, even in a state of rest.

While proton pump inhibitors used for reducing stomach acidity are specifically designed to interact only with proton pumps of the parietal cells, a study shows they also interact non-specifically with other proton pumps in the body and cause their loss of function.

PPIs Hurt Our Gut Bacteria and Impact Immunity

PPI Side effects

PPI Side effects

The good bacteria in our bodies are nurtured by the right biochemical reactions within the digestive tract. This includes the production of sufficient amount of high-quality acid in the stomach.

PPI use alters the gut microflora. Due to low acidity, many unwanted and potentially harmful bacteria increase in numbers while the population of beneficial bacteria decreases. Low stomach acidity favors the growth of opportunistic pathogens like E. coli, Enterococcus, Streptococcus and Staphylococcus. Stomach acidity functions as an immune barrier and any potential pathogen that enters the body through contaminated food or water are killed in the acid. Low acidity fails to kill such pathogens and infections might occur easily in individuals using acid blockers.

Proton Pump Inhibitors: The Final Verdict

Apart from all the health complications cited above, PPI overuse can also increase the risk of cardiovascular diseases. If an individual stops taking PPIs, they experience what is known as rebound reflux, which is reflux coming back with a vengeance.

The problem is that these drugs do not treat the condition at its root and only provide relief from immediate symptoms. For treating acid reflux, it is important to understand the underlying causes of gerd from a holistic viewpoint and make lifestyle and dietary changes to prevent it.

While you become more aware of the foods and habits that trigger your acid reflux and work with a functional medicine practitioner to reverse the condition, there are dietary supplements that help with acid reflux symptoms.

Raft-forming Alginates, which is a combination of seaweed and sodium bicarbonate, can provide instant relief from acid reflux. They do so not by reducing acid production, but by forming a ‘raft’ on the stomach contents, preventing backflow or reflux. This way, you get relief from acid reflux without reducing stomach acid.

Just remember: The real cure for all chronic ailments, including acid reflux or GERD, lies in lifestyle change. Depending on prescription medications is not a viable alternative to living a proper lifestyle.

Jitendra Rathod
Jitendra is a microbiologist and a passionate student of the human body. He is a firm believer in the power of alternative and holistic medicine. He believes nature holds the key to restore us back to health and balance.


Hypomagnesemia Clinical Presentation


Cognitive impact after short-term exposure to different proton pump inhibitors: assessment using CANTAB software


Recognizing Proton Pump Inhibitor Risk


Overutilization of proton-pump inhibitors: what the clinician needs to know


Association of Proton Pump Inhibitors With Risk of Dementia


Hypomagnesaemia due to proton-pump inhibitor therapy: a clinical case series


Omeprazole Therapy Causes Malabsorption of Cyanocobalamin (Vitamin B12)


Effect of antacid and H2 receptor antagonists on the intestinal absorption of folic acid.


Gastric acid secretion in chronic iron-deficiency anaemia.


Omeprazole and bafilomycin, two proton pump inhibitors: differentiation of their effects on gastric, kidney and bone H(+)-translocating ATPases.


Proton pump inhibitors alter the composition of the gut microbiota


Systematic review of the risk of enteric infection in patients taking acid suppression.