CJS INRA ELIGIBLE *

Date : 14/04/2010

Laboratory

MICALIS INRA, UMR 1319
Domaine de Vilvert 78352 Jouy en Josas
Director : Stéphane Aymerich

PhD Supervisor

Maarten Van de Guchte
email : Cet e-mail est protégé contre les robots collecteurs de mails, votre navigateur doit accepter le Javascript pour le voir
phone : +33 134652528

  Subjects / Tools-Methodologies

  1 : Construction of reference gene catalog/Bioinformatics
2 : Food - microbiota - host phenotype correlations/Statistics
3 : Metabolic pathway analysis/Biology and Bioinformatics

(*) Available funding : CJS INRA ELIGIBLE
This project may be selected to be founded by a 5-year grant from INRA (Early stage scientist contract)

Summary of lab's interests

The INRA research institute Micalis situated in Jouy en Josas employs about 90 permanent scientists, 130 other staff, and 60 temporary employees (Ph.D. students and post doctorates), in three departments: Food and gut microbial ecosystems, Systems biology, and Risk. Research in the first of these departments focuses on food - microbiota - host functional interactions, joining forces of long term expertise in microbiology, molecular biology, cell biology and animal experimentation.
Members of this department have been at the forefront of studies on the biodiversity of the microbiota of the human gastro-intestinal (GI) tract, and today several teams in the department take part in the European research project MetaHIT (Metagenomics of the Human Intestinal Tract; http://www.metahit.eu) which was initiated in the department. This project takes metagenomic studies of the GI tract to a new level, with regard to both the quantity of data produced and the development of innovative approaches. The central objective of this particular project is to establish associations between the genes of the human intestinal microbiota and human health or disease.
In this and similar projects, the ecosystems department aims to go beyond the description and correlation analysis of microbiota diversity, to study and understand the functional role of the microbiota in the development and functioning of the host organism. The project presented in this proposition makes part of that global objective.

Summary of project

The project presented here makes part of a collaboration with the INRA division \"Animal Physiology & Livestock Systems\", and aims to develop metagenomic approaches to characterize the microbiota of the bovine rumen and its role in feed conversion efficiency and environmental impact of livestock.

Background. Ruminants are characterized by the possession of a particular digestive system which allows them to efficiently assimilate plant materials. In response to growing demands, the numbers of ruminant livestock steadily increase and pose several environmental issues. Among these are the utilization of resources, the contribution to nitrogen pollution of water and soil, and the contribution to global warming through the production of the greenhouse gas methane. At the same time, ruminants offer a number of important advantages, notably because of their capacity to transform plant material and because they can be reared on land that cannot be used for the cultivation of food crops.

Aim of the Project. The microbiota of the rumen is considered a determining factor for the efficiency of the particular digestive metabolism of ruminants as well as the accompanying environmental problems. The microbiota is composed of a high number of different species of microorganisms that are present in varying quantities and contribute different functions. The present project aims to develop metagenomic approaches to characterize the rumen microbiota (at the level of species, genes, and functions) and associated phenotypes, in order to identify the factors that may be influenced to improve the functioning of the rumen and limit undesirable environmental effects.

Methods. High throughput sequencing of 100 bovine rumen metagenomic samples, covering different groups of animals, different environments and different feeding regimes, is under way. The successful applicant for this project will employ bioinformatics and statistical methods to treat the data, including: 1) the elaboration of a reference gene catalog of the bovine rumen metagenome (cf the publication of the MetaHIT consortium (Nature (2010) 464:59-65) for the human GI tract equivalent), 2) quantitative metagenomic analyses and correlation with physiological, genetical and environmental data, 3) metabolic reconstruction with an emphasis on H2 production and utilization including methane production. Additional analyses will be elaborated and performed in interaction with the project partners and the applicant.