Characterization of the functional link between microbiota and digestive immune system development in early fed rabbits by transcriptomic and metagenomic approaches, identification of new genes of interest by innovative phylogenetic methods

Job Type:

Duration: 24 months
Expected date of fellows recruitment: 2017
Host institution: INRA (the French National Institute for Agricultural Research)
Research Unit: UMR1388 GenPhySE ; Full address: Chemin de Borde Rouge, 31326 Castanet Tolosan, France : Web address:

Abstract: Main improvements of breeding now depend on health management in a limited antibiotic use context. Microbial colonization in neonates affects host development and especially GALT (Gut-Associated Lymphoid Tissue, the gastrointestinal tract’s immune system) development. The objective of the present project is to steer the microbiota in order to optimize immune system development. The goal of the project is to handle the colonization of the digestive ecosystem using a specific food distributed to rabbit pups into the nest, to install an early dialogue with the gastrointestinal immune system and therefore to improve the robustness of the young rabbits. The scientific strategy relies on three solid assumptions based on scientific evidences: 1. Young rabbit are able to express an early feeding behavior; 2. Microbiota implantation is dependent on solid feed intake; 3. Digestive immune system is under microbiota control. While the overall project integrates different components (behavior, nutrition, microbial ecology, immunology), the applicant contribution will focus on whether the alteration of the microbiota associated with feeding modification can impact the development of the digestive immune system in young rabbits. First, the applicant will conduct a transcriptomic analysis on GALT from rabbits with different timing of access to feed to assess the development of their digestive system. Second, the functional link between the microbiota and the digestive immune system development will be investigated using an integrative strategy combining transcriptomic and metagenomic approaches. Finally, potential new important genes for the digestive immune system development will be identified using innovative evolutionary approaches. Overall, this project will lead to new insights about the control of microbial colonization and a better understanding of the early dialog that happens between a host and its symbiont during the immune system development.

Scientific field and subject: Biology, Bioinformatics, Biostatistics, Microbial Ecology
Eligibility criteria (
• Hold a PhD (or PhD will have been awarded by mobility start date);
• Have less than 10 years' research experience after their PhD;
• Not have spent more than 12 months in France within the last 3 years immediately prior to the
• Be able to write and speak fluent English or French;
Applications (in English) should contain the following documents:
• A detailed curriculum vitae with List of publications
• Cover letter mentioning the reference number
• Description of past research experience and how future interests complement the proposed role
• Name and addresses of 2 referees

Sylvie dot Combes at toulouse dot inra dot fr