Dyspepsia and the microbiome: time to focus on the small intestine

We note with interest two recent publications in Gut regarding alterations to the gut microbiome in individuals on proton pump inhibitor (PPI) therapy.1 ,2 With PPI use, both studies observed an increase in oral bacteria in the stool. These changes overlap with those described in patients with cirrhosis of the liver.3 However, very little is known about the impact of this dysbiosis over the length of the GI tract, and how it may link to gut function. While the data from both Jackson et al 1 and Imhann et al 2 are demonstrative of a shift towards oral-associated bacteria, it is important to note that many of these bacteria have also been identified in the stomach and small intestine. Recently, we have shown that although the microbiota found in the healthy duodenum are taxonomically similar to the oral microbiota, their presence and association with the intestinal mucosa is not merely a result of luminal contamination.4 Thus, small intestinal dysbiosis and its potential impact on the gut must also be considered. Compared with studies …