In vivo analysis of the viable microbiota and Helicobacter pylori transcriptome in gastric infection and early stages of carcinogenesis
Journal article, 2017

Emerging evidence shows that the human microbiota plays a larger role in disease progression and health than previously anticipated. Helicobacter pylori, the causative agent of gastric cancer and duodenal and gastric ulcers, was early associated with gastric disease, but it has also been proposed that the accompanying microbiota in Helicobacter pylori-infected individuals might affect disease progression and gastric cancer development. In this study, the composition of the transcriptionally active microbial community and H. pylori gene expression were determined using metatranscriptomic RNA sequencing of stomach biopsy specimens from individuals with different H. pylori infection statuses and premalignant tissue changes. The results show that H. pylori completely dominates the microbiota not only in infected individuals but also in most individuals classified as H. pylori uninfected using conventional methods. Furthermore, H. pylori abundance is positively correlated with the presence of Campylobacter, Deinococcus, and Sulfurospirillum. Finally, we quantified the expression of a large number of Helicobacter pylori genes and found high expression of genes involved in pH regulation and nickel transport. Our study is the first to dissect the viable microbiota of the human stomach by metatranscriptomic analysis, and it shows that metatranscriptomic analysis of the gastric microbiota is feasible and can provide new insights into how bacteria respond in vivo to variations in the stomach microenvironment and at different stages of disease progression.

Atrophic gastritis

Gastric carcinogenesis

Stomach microbiota


Helicobacter pylori


Kaisa Thorell

Karolinska University Hospital

University of Gothenburg

Johan Bengtsson-Palme

University of Gothenburg

Oscar Hsin Fu Liu

University of Gothenburg

Reyna Victoria Palacios Gonzales

Hospital Salud Integral

Intawat Nookaew

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

L. Rabeneck

University of Toronto

L. Paszat

University of Toronto

D. Y. Graham

Baylor College of Medicine

Jens B Nielsen

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Samuel B Lundin

University of Gothenburg

University of Western Australia

Åsa Sjöling

Karolinska University Hospital

University of Gothenburg

Infection and Immunity

0019-9567 (ISSN) 1098-5522 (eISSN)

Vol. 85 10 e00031-17

Subject Categories

Biological Sciences



More information

Latest update