Project
Internship: Analysis of microbes in tissues of different cancer types regarding the presence of antimicrobial resistance genes and virulence factors
Background and research interests – Cancer is a multi-factorial disease involving multiple human cell pathways. Lately, it has been understood that bacteria can affect tumorigenesis or interact with cancer cells. It is expected bacteria resistant to antimicrobials with a high repository of virulence genes will be the ones to promote or influence cancer progress. Many previously associated pathogens were detected in cancer such as melanoma, glioblastoma, low-grade glioma and others. Currently, datasets of metagenomics and metatranscriptomics of cancer microbiome and health tissue are available. However, the analysis of the different bacteria species focuses on antimicrobial-resistant mechanisms and virulence genes. We would like to use commonly applied Bioinformatics tools regarding (meta) genomics analysis, antimicrobial resistant genes and virulence factors description to analyse microbial data in cancer types. Due to the complexity and the vast amount of information, big data analysis principles will be applied. Such valuable datasets can lead to revolutionary conclusions regarding bacteria and cancer interactions.
Objectives
The aims of the study are to:
- Analysis of the microbial data in cancer types regarding antimicrobial-resistant genes and virulence factors
- Expression data information regarding the antimicrobial-resistant genes and virulence factors
- Comparison among different bacterial species, cancer types and healthy tissues.
Methodology / what students can learn
The student will analyse in detail bacterial diverse omics data and integrate the information for conclusions about different bacterial mechanisms.
The student will learn to and be expected to develop, execute, manage, report and complete the research plan developed in collaboration with EMC.
Requirements
We are looking for Bioinformatics MSc students interested in developing their analytical research skills more advanced analytical techniques. The student should be proficient in python and R. The project will have a duration of >= 6 months.
Contact information
Andrew Stubbs, Pathology and Clinical Bioinformatics – a.stubbs@erasmusmc.nl
Nikolaos Strepis, Medical Microbiology- n.strepis@erasmusmc.nl
Peter van Baarlen, Host-Microbe Interactomics, Animal Sciences - (WUR) peter.vanbaarlen@wur.nl
John Hays, Medical Microbiology - j.hays@erasmusmc.nl .