Société Française de Bioinformatique

Mots-Clés

microbiote intestinal alimentation santé digestive

Description

DESCRIPTION OF THE PHD PROGRAM
- Location : INRAE, Jouy-en-Josas –MetaGenoPolis (MGP)
You will join MetaGenoPolis (MGP), an INRAE research unit founded over 10 years ago to:
i) accelerate the generation of fundamental knowledge on gut microbiome–diet–health interactions,
and ii) facilitate the transfer of scientific advances from academia to stakeholders in the socioeconomic
sector. This dual mission is reflected in MGP’s strong research track record, with over
140 scientific publications and more than 150 collaborative projects with private partners from the
agri-food and pharmaceutical sectors. MGP has also fostered the creation of three start-ups.
MGP leads the French Gut project, launched in 2022 in partnership with AP-HP and a public–
private consortium. This ambitious initiative aims to characterize the diversity of gut microbiomes in
the general French population and explore their links with diet and health.

• Supervision :
  PhD Supervisor: Patrick Veiga (INRAE), associate supervisor Marion Leclerc (INRAE)
  Co-supervisors: Sébastien Fromentin (MGP), Fabien Wuestenberghs (AP-HP)
  Duration : 36 months (starting in Fall 2025)
  Scientific background: Digestive disorders impact up to 60% of the French population and significantly influence eating behaviours, particularly through the exclusion of fibre-rich plant-based foods. These dietary restrictions exacerbate a widespread fibre deficiency, compromising public health. This doctoral/PhD research project lays the groundwork for an innovative approach in preventive and personalised medicine, aiming to identify mechanisms associated with the presence of digestive symptoms in the population, especially those involving diet and the gut microbiota.

• Scientific challenges: Understanding the nutritional/dietary and microbial levers in order to mitigate digestive symptoms in the general population and promote healthy and sustainable diet. Deliver an integrated framework of the potential mechanisms of action involved in symptom generation.

• Project objectives and methodology:
  WP1: Stratify the French general population based on digestive symptoms, psychological factors, lifestyle, diet, and gut microbiome features.
  WP2: Assess the impact of clinical factors (e.g., antibiotic use, proton pump inhibitors, history of infections) on the presence of digestive symptoms.
  WP3: Identify specific microbial mechanisms linked to digestive symptoms by reconstructing metabolic pathways related to fiber and FODMAP degradation.
  WP4: Determine the predictive role of the gut microbiota in the presence of digestive symptoms, particularly irritable bowel syndrome, and the associated care pathway.
  These objectives aim to deepen our understanding of how gut microbiota, lifestyle, and clinical factors interact to influence digestive health, potentially leading to more personalized and effective intervention.
  Methodology: The project will be based on advanced analyses in multivariate statistics, and unsupervised clustering, as well as metabolic reconstruction. The available datasets are i) shotgun
  metagenomic data from the national cohort “Le French Gut” (over 25 000 participants to date), ii) self-reported health and lifestyle questionnaires, iii) Food Frequency Questionnaires, iv) the National Health Data System (SNDS).

• Knowledge to be acquired during the PhD:
  Proficiency in R;
  Knowledge of Python is a plus;
  Expertise in univariate and multivariate analyses (including machine learning);
  Querying databases and awareness of health data processing (training in ISO 27001 standard and authorization for SNDS);
  Mastery of nutritional concepts to integrate available nutritional data;
  Basic knowledge to be acquired on the pathophysiology of certain diseases;
  Project management and collaboration within a public-private consortium;
  Training in ISO 9001 standard (MGP).

• Candidate profile:
  Master’s degree (or equivalent) in bioinformatics, nutrition, biology, microbiology, applied statistics, or a related field;
  Strong interest in gut microbiota, nutrition, analysis of complex datasets, and digestive health;
  Scientific integrity, analytical mindset, and ability to work in a multidisciplinary team.
  Resources and facilities :
  Access to a powerful computing cluster (4 petabytes of storage, high-performance processing capacity);
  Access to microbial gene catalogs (metagenomics);
  Access to analysis tools developed within the MetaGenoPolis Unit;
  Technical and methodological support from a multidisciplinary team;
  Access to National Health Data System (SNDS)

• Partners :
  This project is supported by the “Le French Gut” consortium, gathering prestigious academic partners (INRAE, INSERM, APHP, AgroParisTech, CEA, Institut Pasteur) and major industrial players in the field of nutrition and health.

• Application :
  Please send your application (CV, cover letter, and list of publications) to marion.leclerc@irnae.fr
  before June 30th, 2025.