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Dyspepsia and the microbiome: time to focus on the small intestine
  1. Laurie Zhong1,2,3,
  2. Erin R Shanahan2,3,4,
  3. Ashok Raj2,3,
  4. Natasha A Koloski2,5,
  5. Linda Fletcher2,3,
  6. Mark Morrison4,
  7. Marjorie M Walker5,
  8. Nicholas J Talley5,
  9. Gerald Holtmann2,3
  1. 1School of Population Health, University of Queensland, Brisbane, Queensland, Australia
  2. 2Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Translational Research Institute, Woolloongabba, Queensland, Australia
  3. 3School of Medicine, University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
  4. 4Microbial Biology and Metagenomics Research Group, Diamantina Institute, University of Queensland, Brisbane, Queensland, Australia
  5. 5Faculty of Health and Medicine, University of Newcastle, Newcastle, New South Wales, Australia
  1. Correspondence to Dr Erin R Shanahan, Gastroenterology Research, Level 5, Translational Research Institute, 37 Kent St, Woolloongabba QLD 4102, Australia; e.shanahan{at} and ERS contributed equally.

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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 al1 and Imhann et al2 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 …

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  • Contributors LZ and ERS: data acquisition and analysis, writing and editing of manuscript. AR: data acquisition and patient recruitment. NAK: ethics and patient recruitment. LF: data acquisition and supervision. MM: study design, obtained funding, critical review of manuscript. MMW, NJT and GH: study concept and design, obtained funding, critical review of manuscript.

  • Funding We would like to acknowledge the project support of the Princess Alexandra Hospital (PA) Research Foundation and the NHMRC (APP1084544).

  • Competing interests None declared.

  • Ethics approval Metro South Health Human Research Ethics Committee; The University of Queensland Medical Research Ethics Committee. Written consent was obtained from all participants.

  • Provenance and peer review Not commissioned; internally peer reviewed.