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Investigation of oral, gastric, and duodenal microbiota in patients with upper gastrointestinal symptoms
  1. Jorge Cervantes1,
  2. Majd Michael1,
  3. Bo-Young Hong2,
  4. Aden Springer1,
  5. Hua Guo1,
  6. Burgandy Mendoza1,
  7. Mingtao Zeng1,
  8. Olof Sundin3,
  9. Richard McCallum1
  1. 1Texas Tech University Health Sciences Center El Paso Paul L Foster School of Medicine, El Paso, Texas, USA
  2. 2The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
  3. 3Texas Tech University, Lubbock, Texas, USA
  1. Correspondence to Dr Richard McCallum, Internal Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, Texas 79905, USA; richard.mccallum{at}


Disease-associated alterations of the intestinal microbiota composition, known as dysbiosis, have been well described in several functional gastrointestinal (GI) disorders. Several studies have described alterations in the gastric microbiota in functional dyspepsia, but very few have looked at the duodenum.

Here, we explored the upper GI tract microbiota of inpatients with upper GI dyspeptic symptoms, and compared them to achalasia controls, as there is no indication for an esophagogastroduodenoscopy in healthy individuals.

We found differences in the microbiota composition at the three sites evaluated (ie, saliva, stomach and duodenum). Changes observed in patients with dyspepsia included an increase in Veillonella in saliva, an oral shift in the composition of the gastric microbiota, and to some degree in the duodenum as well, where an important abundance of anaerobes was observed. Metabolic function prediction identified greater anaerobic metabolism in the stomach microbial community of patients with dyspepsia. Proton pump inhibitor use was not associated with any particular genus. Co-abundance analysis revealed Rothia as the main hub in the duodenum, a genus that significantly correlated with the relative abundance of Clostridium, Haemophilus, and Actinobacillus.

We conclude that patients with upper GI symptoms consistent with dyspepsia have alterations in the microbiota of saliva, the stomach, and duodenum, which could contribute to symptoms of functional GI disorders.

  • microbiota
  • gastric mucosa
  • duodenum

Statistics from


  • Contributors RM: Study conceptualization. MM, RM: Sample collection and medical procedures.

    AS, HG, BM, OS: Conducted Experiments. B-YH, JC: Performed analysis. JC, RM: Wrote the manuscript.

  • Funding The authors have not declared a specific grant for this research from any funding agency in the public, commercial or not-for-profit sectors.

  • Competing interests None declared.

  • Patient consent for publication Not required.

  • Ethics approval This study was approved by Institutional Review Board at Texas Tech University Health Science Center.

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

  • Data availability statement Data are available upon reasonable request.

  • Supplemental material This content has been supplied by the author(s). It has not been vetted by BMJ Publishing Group Limited (BMJ) and may not have been peer-reviewed. Any opinions or recommendations discussed are solely those of the author(s) and are not endorsed by BMJ. BMJ disclaims all liability and responsibility arising from any reliance placed on the content. Where the content includes any translated material, BMJ does not warrant the accuracy and reliability of the translations (including but not limited to local regulations, clinical guidelines, terminology, drug names and drug dosages), and is not responsible for any error and/or omissions arising from translation and adaptation or otherwise.

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