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24, chemin de Borde Rouge -Auzeville - CS52627 31326 Castanet Tolosan cedex - France

Last update: May 2021

Menu Logo Principal AgroParisTech Université Paris-Saclay SAPS - Sciences Animales Paris-Saclay


GABI : Génétique Animale et Biologie IntégrativeUnité Mixte de Recherche INRA - AgroParisTech

Genetics, Microbiota, Health Team

Leader: Fanny Calenge



Our team has developed expertises for its studies on functional genomics, metagenomics and immunophenotyping.

Overall activities

The GeMS team studies interactions between genetic variations in the host, the intestinal microbiota and immunity, and their effects on health and robustness in pigs and chickens. In order to do so, it couples “omics” approaches with fine and/or high-throughput immuno-phenotyping, in vivo and in vitro.

Outstanding results

  • Annotation of the genomes of several domestic animal species
  • Identification of porcine enterotypes.
  • Publication of a catalogue of the porcine intestinal metagenome.

Scientific questions

1-  The genetic control of immunity and immunocompetence

We study the genetic architecture of health and welfare traits in the pig and chicken by evaluating the capacity of the animals to mount an efficient immune response after infection by pathogens, after vaccination, or during weaning in piglets. We also study the trade-offs between immunocompetence and production traits. Finally, we use a functional approach on the MeLiM porcine model to understand the implication of host immunity in the regression of cutaneous melanoma. We use genetic and functional genomics approaches in large experimentations; we use classical ex vivo immunophenotyping; and we develop methods for in vitro phenotyping (organoids, cell lines).

  •    Related projects: SAPHIR (Europe) ; PigletBiota (ANR) ; SalmoCar (Carnot); MiniSRegress (Inca)

2- Impact of the intestinal microbiota on animal health

The animal and its microbiota form a symbiotic organism called the holobiont. The intestinal microbiota plays a central role in health, notably through its interactions with the immune system. Our projects study the contribution of the microbiota in the host’s health phenotypes and the genetic control of the host on the intestinal microbiota. We have created a metagenome catalogue in the pig and chicken in order to use quantitative and functional metagenomics approaches.

  •    Related projects: Galmide (MP GISA) ; SalmoCar (Carnot) ; PigletBiota (ANR) ; SAPHIR (Europe).

3 – Functional genomics and health

We carry forth functional genomics studies as part of the international FAANG initiative ( By using different molecular approaches (tridimensional organization of the genome, epigenetics modifications and accessibility of chromatin, transcript catalogues, etc), we seek to identify the regulating elements of the genome. We are using this in-depth knowledge of how genomes work to contribute to our integrative study of the relation between genotype and phenotype. In fact, we develop innovative cell tools (organoids, pluripotent cells) to facilitate the functional validations of candidate variants using genome editing and ex vivo phenotyping

  •    Related projects: GENE-SWitCH ; Galmide ; SAPHIR ; PIgletBiota, PluS4Pig, SNOOPY, CatCHI 

Research tools

  • Experiments with the GenESI (Le Magneraud; pig) and PEAT and PFIE (Nouzilly; chicken) experimental farms.
  • In charge of the experimental facilities at Jouy-en-Josas housing pigs for biomedical studies including the MeLiM pig.
  • Production of genomics data with INRAE @BRIDGe, Jouy-en-Josas and GeT-PlaGe, Toulouse and metagenomics data with MetaGenoPolis.


The GeMS team collaborates with other teams from GABI, INRAE research units belonging to several divisions (GA, PHASE, SA, MICA)) and national and international academic partners. The team also has partnerships with industrial actors (selection, the animal food industry, and the pharmaceutical industry).

  • Member of the following doctoral school: SDSV (Structure et Dynamique des Systèmes Vivants)     
  • Member of the University Paris-Saclay