Master 2 Internship in microbial and computational ecology

 Stage · Stage M2  · 6 mois    Bac+5 / Master   INRAE MICALIS · Jouy en Josas (France)  Gratification réglementaire de la fonction publique pour stages de Master 2 (environ 600 euros/mois)

 Date de prise de poste : 1 février 2024


food microbial ecology metabolic reconstruction metagenomics bioinformatic workflows development



You will be welcomed in the Food Microbial Ecology or FME lab (, which is part of

the Micalis unit – Food and Gut Microbiology for Health - (Joint Research Unit INRAE-AgroParisTech located

in Jouy-en-Josas, Yvelines, Ile-de-France). The FME team develops microbial ecology approaches to food

microbiota and its activities are declined according to four types of research: 1) To obtain a holistic view of

food microbiota in the food chain; 2) To improve the functional analysis of metabolic interactions of food

microbes; 3) To develop synthetic food microbial ecology methodologies; 4) To study the interactions

between food and gut microbiota

Understanding food microbiomes' functional diversity involves isolating specific metabolic functions and species of interest from vast arrays of microorganisms. Metabolic reconstruction tools become essential in this quest. It allows functional screening of genome-scale metabolic networks (GSMNs) at genomic levels, accurately charting individual and shared metabolic attributes. Key community species are identified, ensuring streamlined GSMN reconstruction and metabolic cooperation assessment across species. In addition, metabolic reconstruction tools can help simplify expansive microbiota into smaller, functionally consistent communities. Leveraging an interdisciplinary approach encompassing microbial ecology, omics data, and computational biology, the FME lab aims to delve deep into these microbial interactions. However, a noticeable gap remains in seamlessly integrating metagenomic databases with metabolic reconstruction networks, especially in the context of fermented foods' potential benefits for gut health.


This internship project aims to develop an automated system that chains metabolic reconstruction networks with in-house metagenomic software, especially concerning the food microbiome and its interaction with the gut microbiome.

  1. Integrate public and internal food metagenomic studies with metabolic reconstruction tools.
  2. Apply the developed system to fermented foods to predict their impact on gut microbiome metabolite production.



  1. Collect public data and perform an initial metagenomic analysis on fermented foods using existing team pipelines.
  2. Develop and test an integrated system connecting metagenomic data with metabolic network reconstruction using the M2M tool.
  3. Analyze metabolic capabilities in selected fermented foods and evaluate potential benefits to gut health.



By joining our teams, you benefit from:

sports and cultural activities;
- collective catering.



Knowledge of statistics for high-throughput biological data analysis, bioinformatics, and biology (genomics & metagenomics, microbiology).

Proficiency in the R or Python programming language. Knowledge of workflow managers like Snakemake is recommended.

Fluency in English (read required, written if possible).



Procédure : Envoyer une lettre de motivation et un CV.

Date limite : 29 décembre 2023


Julien Tap

Offre publiée le 23 octobre 2023, affichage jusqu'au 29 décembre 2023