A postdoctoral researcher position is available at Laboratoire National de Santé to conduct metagenomics experiments as part of the “CampylOmic” research project funded by the FNR. The objective is to develop a culture-independent genotyping method to assess the population diversity of C. jejuni in environmental samples from metagenomic data. The postdoc will be part of the Epidemiology and Microbial genomics team.

Main activities:

• develop a metagenomic protocol to assess the diversity in alleles of the 7 MLST housekeeping genes of Campylobacter jejuni in faecal material from animals or environmental samples
• test the method on pure culture and spiked samples
• optimize the DNA extraction of samples
• implement metagenomic analysis pipelines – develop and/or apply existing metagenomics bioinformatics tools
• develop a targeted sequencing approach to identify host species from the animal faecal sample (DNA barcoding approach)
• apply the optimized method on a collection of approximatively 300 samples

Desired profile:

• the candidate will have a PhD in microbiology, molecular biology, computational biology, bioinformatics, microbial genomics or related fields, and experience in high throughput genomic technologies including metagenomics
• the candidate will be fluent in English, fluency in French is an asset

Requirements:

• knowledge in foodborne pathogens genotyping and culture of Campylobacter isolates are assets
• Linux, Python or R programming skills
• knowledge of open source and commercial microbial NGS analysis pipelines (Seqsphere, Bionumerics, CGE Toolbox, Geneious)

If you meet the above profile requirements and wish to apply, please send your application (CV, letter of intent and copies of your degrees) with the reference 2018-CampylOmic-01. The applications will be treated in order of arrival and with the highest degree of confidentiality.