WMS/SLS Micro Seminar: Around the world and in the stomach with Helicobacter pylori, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet
As Helicobacter pylori displays an extensive intra-species diversity, genomics is a powerful tool to understand evolution and mechanisms of virulence. Generating large amounts of whole-genome sequencing (WGS) data is however not sufficient, but to produce genomes of high quality with careful annotation and detailed metadata is also crucial to be able to draw biologically and clinically relevant conclusions. To facilitate this we collected all publically available H. pylori WGS data together with available metadata in a BIGS database. In addition to this, we performed a focused sequencing effort, generating in total 450 new draft genomes from different parts of the world, with an emphasis on Europe and the Americas. The resulting database, consisting of over 1500 genomes has allowed us to dig deeply into several interesting aspects of H. pylori biology and evolution, including an expansion of our previous comparative genomics efforts of H. pylori isolates from the American continent, ranging from Northern Canada to Chile in the South, and what implications the mixing of ancestries from European, African, Asian and Old World Amerind sources may have on regional virulence patterns.
In addition to studying the genomic aspects of H. pylori we are also interested in more functional aspects of the host-microbe interaction in the human stomach. To study this, we performed RNA sequencing of stomach biopsies from individuals with various gastric disease, ranging from non-atrophic gastritis to the precancerous lesions corpus atrophy and intestinal metaplasia. This way, we could both investigate the composition of the transcriptionally active microbial community and the H. pylori gene expression.
I have a background in Biomedical Sciences from Lund University, Sweden and defended my PhD entitled “Multi-level characterization of host and
pathogen in Helicobacter pylori-associated gastric carcinogenesis” at University of Gothenburg/Chalmers University of Technology in 2014. After three years as a Postdoctoral researcher in the lab of Lars Engstrand at Science for Life.
Laboratory/Karolinska Institutet, Stockholm, I have now returned to Gothenburg to pursue my own projects. In my career I have gradually moved from being a mainly experimental researcher with the focus on the human side of cancer development, to bioinformatics and analyses of bacterial genomics, with an emphasis on Helicobacter pylori.