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In vivo analysis of the viable microbiota and Helicobacter pylori transcriptome in gastric infection and early stages of carcinogenesis.

Journal article
Authors Kaisa Thorell
Johan Bengtsson-Palme
Oscar Hsin-Fu Liu
Reyna Victoria Palacios Gonzales
Intawat Nookaew
Linda Rabeneck
Lawrence Paszat
David Y Graham
Jens Nielsen
Samuel B Lundin
Åsa Sjöling
Published in Infection and immunity
Volume 85
Issue 10
ISSN 1098-5522
Publication year 2017
Published at Institute of Biomedicine, Department of Microbiology and Immunology
Centre for antibiotic resistance research, CARe
Institute of Biomedicine, Department of Infectious Medicine
Language en
Subject categories Cancer and Oncology, Microbiology in the medical area


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 the H. pylori gene expression was determined using metatranscriptomic RNA sequencing of stomach biopsies from individuals with different H. pylori infection status and pre-malignant 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 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 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.

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