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.
Metatranscriptomics
Atrophic gastritis
Helicobacter pylori
Gastric carcinogenesis
Stomach microbiota
Author
Kaisa Thorell
Goteborgs universitet, Institutionen for biomedicin
Karolinska University Hospital
Johan Bengtsson-Palme
Goteborgs Universitet
Goteborgs universitet, Institutionen for biomedicin
Oscar Hsin Fu Liu
Goteborgs universitet, Institutionen for biomedicin
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
Goteborgs universitet, Institutionen for biomedicin
University of Western Australia
Åsa Sjöling
Karolinska University Hospital
Goteborgs universitet, Institutionen for biomedicin
Infection and Immunity
0019-9567 (ISSN) 1098-5522 (eISSN)
Vol. 85 10 e00031-17Subject Categories (SSIF 2011)
Biological Sciences
DOI
10.1128/IAI.00031-17