Master 2 Recherche - Stage sur l'analyse du microbiome dans les maladies auto-immunes et auto-inflammatoires

Type de poste
Niveau d'étude minimal
Durée du poste
Contrat renouvelable
Contrat non renouvelable
Date de prise de fonction
Date de fin de validité de l'annonce
Nom de la structure d'accueil

Hôpital de la Pitié-Salpêtrière
83, boulevard de l'Hôpital
75013 Paris

Nicolas Tchitchek
Adrien Six
Email du/des contacts

Title: Microbiome analysis of autoimmune and autoinflammatory disorders


The i3 laboratory, located at the Hospital of the Pitié-Salpêtrière in Paris, launched in 2015 an observational clinical trial (Transimmunom – NCT02466217) which aims at studying 19 autoimmune and autoinflammatory disorders. The final goal is to guide the development of novel therapeutic strategies and to redefine the nosography of autoimmune and autoinflammatory diseases. Our current strategy is to analyze and to integrate “omics” and clinical data to identify and understand the complexity of the immune responses underlying these immunopathologies by applying systems biology approaches. In particular, we are focusing our investigations on the process and analysis of microbiome (metagenomics), transcriptome (RNA-seq), TCR repertoire (Rep-seq), deep immunophenotyping (flow cytometry), cytokines (Luminex) and clinical data. In this context, the collected intestinal microbiome data are of great importance as multiple studies have outlined its role in the context of autoimmune diseases. Currently, we processed samples from 300 patients (affected by one of the nineteen pathologies) and 50 healthy donors. Data have been generated and stored in dedicated servers. 

The project proposal for a Master 2 internship aims at developing, under the supervision of a bioinformatician and an immunologist, approaches for the analysis of microbiome data collected from gut samples of patients. The selected candidate will rely on an existing pipeline for the processing and first-level analysis (quality control of sequences until OTU quantification) of microbiome data on our collected data (consisting of several hundreds of microbiomes profiles). Furthermore, analytical approaches will be developed to: (i) quantify the diversity of phylum and bacterial species; (ii) to identify bacterial communities impacted by diseases or treatments; and (iii) to integrate these microbiome data with other “omics” or clinical data. Especially, co-expression networks of bacteria abundances will also be constructed to understand the synergy within and between bacterial communities. Such analyses will allow to understand the symbiosis and dysbiosis mechanisms involved in autoimmune and autoinflammatory diseases. The starting date of thhis 6-months internship is flexible.

The expected MSc candidate will justify training in Immunology / Computer Science / Bioinformatics and/or Biostatistics, with interest for Systems Biology. Experience with R tools (or other programming languages) as well as with Linux OS are a plus. The candidate will benefit from an interdisciplinary environment, including biologists, immunologists, clinicians, computer scientists and bioinformaticians. This project is part of the laboratory funded projects (LabEx Transimmunom -,



Nicolas TCHITCHEK ( / Adrien SIX (


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