The Impact of Proton Pump Inhibitors on the Fecal Microbiome

Table 1. Inclusion Criteria for Healthy Volunteers: 1\. Healthy individuals without chronic gastrointestinal problems or using antisecretory medications. Table 2. Inclusion Criteria for Clostridium difficile infection subjects: 1\. Newly diagnosed first episode of CDI prior to being treated. Table 3. Exclusion Criteria for Healthy Subjects: 1. Prior gastrointestinal surgery that has altered the anatomy of the esophagus, stomach, or small/large intestine including appendectomy and cholecystectomy. 2. Chronic daily use of any medications that could alter gastrointestinal secretory or motor function (see Table 2). 3. Gastrointestinal, cardiovascular, endocrine, renal, or other chronic disease likely to affect gastrointestinal motility (e.g., uncontrolled diabetes mellitus). 4. Females of childbearing age who are not practicing at least one form of birth control at least one month prior to starting the PPI or are pregnant or lactating (a pregnancy test will be performed on female subjects prior to PPI use). 5. Significant untreated psychiatric disease. Table 4. Prohibited Medications: 1. Antibiotics within 2 months of the stool sample collection. 2. Probiotics (e.g., Florastor, Align, Flora-Q, VSL#3, lactobacillus, bifidobacterium) within 2 weeks of the stool sample collection. 3. Fiber supplements (e.g., Metamucil, Citrucel, Benefiber), unless maintained on a stable dose for the last 3 months. 4. Chronic use of medications that alter gastric pH: proton pump inhibitors (e.g., omeprazole, lansoprazole, esomeprazole, pantoprazole, rabeprazole, dexlansoprazole) and histamine2 receptor antagonists (e.g., cimetidine, famotidine, ranitidine). 5. Chronic use of medications that affect gastrointestinal motility and/or transit including prokinetic agents (e.g., metoclopramide (Reglan), tegaserod (Zelnorm), domperidone (Motilium), erythromycin), narcotic analgesic agents (e.g., methadone, fentanyl, oxycodone, codeine, morphine, hydromorphone), laxatives including mineral oil, anticholinergic agents (e.g., Bentyl, Levsin), and antidiarrheal agents (e.g., Kaopectate (donnagel), Pepto-Bismol (bismuth subsalicylate), Imodium (loperamide), Lomotil (atropine with diphenoxylate), codeine, tincture of opium).