The preferred medical treatment for reflux or GORD is proton pump inhibitors (PPIs) or other forms of antacid medication.
PPI treatment, at standard effective dosage, almost completely abolishes the gastric acid barrier with an increase in bacterial density higher than 1000-fold and gastric and duodenal bacterial colonisation in more than 50% of patients.
So what does this mean? Taking antacid medication or lowering your stomach acid, allows the ‘bad’ bacteria to take hold. Considering that Helicobacter pylori can only survive and flourish when stomach acid is low, PPIs provide the perfect environment for bacterial overgrowth.
Source: Compare D, Pica l, Rocco A, et al. Effects of long-term PPI treatment on producing bowel symptoms and SIBO. Eur J Clin Invest: 2011 Apr;41(4):380-6
SIBO = small intestine bacterial overgrowth