Metagenomic Analysis of Clinical Samples

Type de poste
Durée du poste
Contrat renouvelable
Contrat non renouvelable
Date de prise de fonction
Date de fin de validité de l'annonce


Sean Kennedy
Dusko Ehrlich
Email du/des contacts
A Postdoctoral position for 2 years is open in the laboratory team of Sean Kennedy and S. Dusko Ehrlich at INRA, Jouy-en-Josas. The successful candidate will join a dynamic and productive team in the ground-breaking field of quantitative metagenomics and will work in close collaboration with the industrial partner Danone Research. Quantitative Metagenomics, developed at INRA, involves the massive sequencing of complex environments using Next Generation Sequencing (NGS) technology. We specifically target the human intestinal tract and use a unique set of bioinformatic tools to at once describe the bacterial community present and to discern potential diagnostic signatures associated with diseases such as obesity, Crohn’s disease, ulcerative colitis and other intestinal or metabolic disorders. Our team has recently published several high-impact manuscripts; Arumugam M. et al. Enterotypes of the human gut microbiome. Nature. 2011:1-7 and Qin J et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464(7285):59-65. The dedicated pipeline is using Windows, Linux and Solaris. The informatics team is developing in house tools using GPU ( The overall objectives of the proposed project is to integrate SOLiD NGS data of microbiome profiles of faecal samples currently available or obtained thought clinical trials. The global objects of this research will be to: - interpret microbiome data sets with the objective to: - identify correlations with IBS symptoms severity - establish the abundance of genes involved in major metabolic pathways relevant for symptoms (e.g. the production of gaseous compounds) - identify the impact of food/probiotic intervention on Gut Microbiome structure - communicate results in a formal manner, accepting leadership and to attend to international meeting - help the informatics team in improving the bioinformatics pipeline for analysis of clinical samples due for 2012 and beyond. In the process of interacting with the informatics and bioinformatics team, the candidate will have the opportunity to propose new tools and new designs. Description of the Candidate: Primary Activities: Interact closely with both biological and informatics personnel from both MetaQuant and Danone Learn to use and implement the various tools in the metagenomic analysis pipeline to respond to the questions posed by the project, and also to explore new avenues of questioning. Participate in group meetings and general discussions at both MetaQuant and Danone Skills Required: The individual selected should be highly organized, rigorous and voluntary to learn informatics and programming. The candidate needs not have programming experience, although demonstrating a programming skill will be highly appreciated. The candidate needs to have basic skill in statistics and bioinformatics.