Effect of the proton pump inhibitor omeprazole on the gastrointestinal bacterial microbiota of healthy dogs as evaluated by molecular techniques

The effect of the proton-pump inhibitor omeprazole on gastrointestinal bacteria was evaluated. Eight healthy 9-month-old dogs (4 males and 4 females) received omeprazole (1.1 mg/kg) orally twice a day for 15 days. Fecal samples and endoscopic biopsies from the stomach and duodenum were obtained on days 30 and 15 before omeprazole administration, on day 15 (last day of administration), and 15 days after the end of administration. The microbiota was evaluated using 16S rRNA gene 454-pyrosequencing, fluorescent in situ hybridization, and qPCR. In the stomach, pyrosequencing revealed a higher bacterial richness (p=0.0021) and a decrease in Helicobacter organisms during omeprazole administration (median: 92%, median before and after: >98%, p=0.0336) which was accompanied by a higher abundance of Firmicutes and Fusobacteria. FISH confirmed this effect of omeprazole on gastric Helicobacter (p<0.0001). In the duodenum, FISH showed an increase in total bacteria (p=0.0033) and pyrosequencing a consistent increase in Lactobacillus and Enterococcus during omeprazole in the male dogs. In feces, qPCR showed an increase in Lactobacillus during omeprazole (p<0.0001), which was accompanied, in the males, by a lower abundance of Faecalibacterium and Bacteroides. This study suggests that orally administered omeprazole can alter the abundance of the gastrointestinal microbiota in healthy dogs.