Functional medicine LupusBefore taking your daily antacid, you might consider how it is affecting the trillions of bugs living in your gut.

A new study just published in the journal Microbiome shows that people who regularly take proton pump inhibitors (PPIs) have less microbial diversity, which increases their risk for opportunistic infections like clostridium difficile and pneumonia, as well as vitamin deficiencies and bone fractures.

“Evidence has been mounting for years that long-term use of proton pump inhibitors poses increased risks for a variety of associated complications, but we have never really understood why,” says John DiBaise, M.D., a Mayo Clinic gastroenterologist and senior author on the study. “What this study does for the first time is demonstrate a plausible explanation for these associated conditions.”

Proton pump inhibitors are prescribed for gastroesophogeal reflux disease (GERD). Patients complain of chest pain, chronic cough, sleep disturbances, and hoarseness. GERD is caused by too much stomach acid production causing it to reflux into the esophagus.

Many epidemiological studies have demonstrated PPIs association to nutritional, metabolic and infectious disorders. Prolonged use of antacids has been associated with anemias, magnesium deficiency, osteoporosis-related fractures, small intestinal bacterial overgrowth (SIBO), and community-acquired pneumonia.

Diet, genetics, and environmental influences all contribute in maintaining a healthy microbiome, which is essential to overall health. The gastrointestinal tract consists of trillions of bacteria. There are over 400 species of microbes in the human intestinal tract far exceeding all other cells in the human body combined. Most of these bacteria are beneficial and support everything from digestion and vitamin synthesis to immune system regulation.

Lifestyle changes and nutritional support may be sufficient to address acid reflux. Patients should eat smaller portions at meals. In addition, avoid laying down after meals and avoid eating before bed. Also, alcohol and specific foods can trigger symptoms.

Although these medications may help with the symptoms, proton pump inhibitors may not be the solution. We typically do not produce more hormones, insulin, and enzymes as we age. The truth is that most of our bodies’ processes decrease as we age. Most people suffering with acid reflux or GERD may be suffering from too little acid called hypochlorhydria, which is when the stomach is unable to produce enough hydrochloric acid.

The barrier that prevents HCL from traveling from your stomach up into your esophagus is called the esophageal sphincter. The cause of this sphincter dysfunction is inadequate levels of hydrochloric acid. Normal acid levels help prevent infection in your gut as well as enhance absorption of vitamins and minerals. Supplementation with betaine HCL will enhance the normal acid levels of the stomach.

Additional supplements may be needed to improve your digestive function such as probiotics and glutamine. Deglycyrrhiizinated licorice (DGL) is well established as an anti-ulcer and mucosal healing botanical and is soothing and protecting to the gastric mucosa and mucous membranes lining the digestive tract.

Helicoacter pylori is a major cause of gastritis. Mastic gum, methylmethionesulfonium, zinc-carnosine and vitamin C address both eradication of H. pylori and the healing and protection of inflamed mucosal tissue.

Natural treatments offer a more effective approach than what is provided by proton pump inhibitors. Proton pump inhibitors can induce several nutrient deficiencies in calcium, potassium, and magnesium. In addition, they can cause serious neuromuscular and cardiovascular problems and increase the chance of hip fracture in people over 50 years of age.


Charlie T Seto, Patricio Jeraldo, Robert Orenstein, Nicholas Chia, John K DiBaise. Prolonged use of a proton pump inhibitor reduces microbial diversity: implications for Clostridium difficile susceptibility. Microbiome, 2014; 2 (1): 42 DOI: 10.1186/2049-2618-2-42

The Annals of Internal Medicine, November 17, 2009, Volume 15.

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