STAGE 6 months Master 2 Internship “Diversity and co-evolution of methanogenic archaea with animal hosts”

Date de mise à jour de l’offre

Institut Pasteur :

In our group we use cutting-edge phylogenomics approaches to study the macroevolutionary processes that led to the current diversity of microorganisms, with an original view on the whole Tree of Life. We are particularly interested in resolving the deepest divergences in both Bacteria and Archaea, reconstructing the evolutionary relationships among the three domains of Life, highlighting the existence of novel and important microbial clades, and dissecting the diversity and evolutionary history of key microbial cellular processes, with an important component of functional annotation and gene discovery, which drives experimental work. Together, our researches allow us to address major evolutionary transitions in the history of life, and to challenge established paradigms in ancient microbial evolution.

Description de la mission

The objectives for this internship are to investigate for the first time the diversity of archaeal methanogens in a large range of animal microbiota, collected in collaboration with the with the Parc Zoologique de Paris. The relative abundance (qPCR) and the composition (Miseq) of archaea and bacteria will be determined in these samples by targeting 16S of bacteria and archaea, and specific markers for methanogens. These sequence data will be treated by in house developed bioinformatics pipelines for OTU determination and taxonomic affiliation. This might identify whether other archaeal lineages in addition to Methanomassiliicoccales and Methanobacteriales are present in the animal digestive tract. Distribution of archaea in animal species will be analyzed to understand if they follow co-speciation or diet patterns (carnivore, herbivore, omnivore). These analyses will be completed by mining public metagenomes of animals for additional archaeal lineages.



During this internship, the candidate will acquire the theoretical and methodological bases for treatment of metataxonomic and metagenomic sequence data, contribute to an understudied and important subject, and increase his/her general culture on the diversity and evolution of archaea.

Profil recherché

The ideal candidate will have a strong interest in ecology and evolution of microorganisms and previous experience with sequence data.



The results will set the basis for selection of samples for de novo sequencing (Hi-Seq) to obtain novel archaeal genomes and eventually isolation/description of new archaeal strains in the frame of a PhD thesis. Combination of functional annotation, comparative genomics and phylogenomics analysis will be used to predict the determinants that led to the adaptation of archaea to the digestive tract. This knowledge will participate to discern the factors controlling the interactions of archaea within the gut microbiota as well as their impact on the host.

Niveau de qualification requis

Bac + 4/5 et +
  • Employeur
    Institut Pasteur
  • Secteur d’activité de la structure
    Enseignement - Formation - Recherche
  • Effectif de la structure
    Plus de 250 salariés
  • Type de stage ou contrat
    Stage d'immersion en milieu professionnel dans le cadre de la formation professionnelle continue
  • Date prévisionnelle de démarrage
  • Durée du stage ou contrat
    Plus de 4 mois et jusqu'à 6 mois
  • Le stage est-il rémunéré ?
    Oui
  • Niveau de qualification requis

    Bac + 4/5 et +
  • Lieu du stage
    25 rue du Docteur Roux
    75015 Paris
  • Accès et transports
    Metro Pasteur (Ligne 6 et 12)