Side effects of proton pump inhibitors (PPI) can be linked to the changes in the intestinal microbiome that occur during therapy, especially in long-term users. Therefore, the microbiome might also be a key player in the reduction of PPI side effects. We tested the effects of a three-month intervention with a multispecies synbiotic on intestinal inflammation, gut barrier function, microbiome composition, routine laboratory parameters and quality of life in patients with long-term PPI therapy. Thirtysix patients received a daily dose of a multispecies synbiotic for three months and were clinically observed without intervention for another three months. After intervention 17% of patients reached normal calprotectin levels; the overall reduction did not reach statistical significance (−18.8 ng/ mg; 95%CI: −50.5; 12.9, p = 0.2). Elevated zonulin levels could be significantly reduced (−46.3 ng/ mg; 95%CI: −71.4; −21.2; p < 0.001). The abundance of Stomatobaculum in the microbiome was reduced and Bacillus increased during the intervention. Furthermore, albumin, alkaline phosphatase and thrombocyte count were significantly increased and aspartate transaminase was significantly decreased during intervention. Gastrointestinal quality of life showed significant improvements. In conclusion, microbiome-related side effects of long-term PPI use can be substantially reduced by synbiotic intervention. Further studies are warranted to optimize dosage and duration of the intervention. In the last 30 years proton pump inhibitors (PPI) have established themselves as highly effective treatment of acid related diseases and became the most often prescribed class of drugs in gastroenterology 1,2. Underneath their immaculate image of gastric protection, however, their side effect profile-although well described by high quality data-remained largely unaddressed 3. Many of the side effects might be rooted in PPI-induced changes of the microbiome (i.e. dysbiosis): increased risk of enteric infections, bloating, flatulence, abdominal pain, stool frequency abnormalities, intestinal inflammation and vitamin B12 malabsorption 4-12. Long term PPI use can introduce ample alterations to the intestinal microbiome: Changes in composition, reduction of alpha diversity, small intestinal bacterial overgrowth and the manifestation of oral bacteria in more distal parts of the intestine have been observed 13-19. A loss of alpha diversity and therefore a loss in pathogen-colonization resistance could account for the increased risk of enteric infections 20,21. The change of composition, which includes the reduction of Clostridiales and the increase of Enterococcaceae and Streptococcaceae, and function of the microbiome might directly predispose for Clostridium difficile infections 22. In children, persistent bowel symptoms during PPI use have been linked to small intestinal bacterial overgrowth 23. The association with the microbiome could be a crucial factor for the amelioration of PPI side effects. Modulating the microbiome with probiotic bacteria might ...