ANR-blanc funded project :

Abstract : Our body surfaces are in close contact with trillions of bacteria, among them 90% inhabit the distal parts of the gastrointestinal tract. One of the major limitations for studying commensal bacteria is our inability to cultivate most microbial species. Recent technical advance, namely metagenomic, has enabled rapid progress in characterizing the genomic and genetic diversities of the gut microbiota. This approach has underscored its highly selected composition, dominated in mammals by bacterial species belonging to few phyla (predominance of Bacteroidetes and Firmicutes). The microbial genome (microbiome) contains ~150 times as many genes as the host genome. Hence, the emerging concept is that the microbiota is an integral component/organ of the host physiology. During millions years of co-evolution, the hosts have developed complex immune mechanisms in order to control this close microbial ecosystem. Accumulating evidence highlighted that the microbiota contributes to local development and tuning of gut homeostasis, shaping of host immune system and maintaining the microbial ecosystem.
Our knowledge on the various contributions of the microbiota to health is still in its infancy and the underlying cellular and molecular mechanisms of its interplay with the host intestinal cells remain poorly understood. The intestinal epithelial cells (IEC) are the first line in contact with microbes and have a key role of in the immune regulation which impact on chronic inflammatory disease. The project focusses on the modulation of the inflammatory processes mediated by the IEC/microbiota dialogue.

We were pioneers in developing a functional metagenomic approach to study microbiota host interactions and have demonstrated that this innovative approach is efficient to identify genes potentially involved in host microbiota cross-talk. Using a high throughput screening platform and the reporter gene-based technology, we will identify bio-active clones from metagenomic libraries able to modulate key targets in intestinal epithelial cells. These targets are the immuno-regulatory relevant genes (TSLP, TGF-beta and RALDH1) and transcription factors NF-kappaB, AP1, and PPARgamma. The study of commensal-host relationship requires bi-directional approaches whereby responses of commensals are identified together with the corresponding host cell responses and relevant effectors. By sequencing and transposon mutagenesis approaches, we will characterize the bacterial genes and the nature of the strain involved in IEC responses. The deep characterization of the cellular responses will be deciphered by human cell transcriptomic analysis. Subsequently, using biochemistry and cell biology, we will identify the bacterial bio-modulator components, the putative host receptor and cellular pathways involved in the interaction with the host cells. Moreover, the integrative study of the dialogue among bacteria, epithelial cells and immune cells in a co-culture approach will allow deciphering the impact of the modulatory components on the host responses. Moreover, we aim at demonstrating the in vivo relevance of the identified mechanisms. For this purpose we will use inflammatory and gnotobiotic mouse models to analyse in vivo the patho-physiological relevance of the identified interactions. Finally, the putative implication of the identified genes in human pathologies will be assessed by monitoring the expression of these genes or the gene-expressing bacteria in healthy donors or in patient with immune-related pathologies.
Altogether this innovative project will allow identifying new bioactive molecular signals from the gut microbiota able to influence the host immune system and characterizing at the molecular level the mechanisms underlying their immunomodulatory properties. Thus, FunMetaGen is geared towards knowledge-based biotechnological developments and nutrition strategies with relevance to health.

Partners of the Project:

Coordinator of the project : Hervé M. Blottière, INRA Micalis

  • Partner 1 : INRA-Micalis in Jouy-en-Josas
Three laboratories and one technical platform are involved in FunMetaGen :
  • The FInE laboratory (Functionality of the Intestinal Ecosystem), directed by J. Doré
  • The Ife laboratory (Interactions of Firmicutes with the Environnement), leaded by Emmanuelle Maguin,
  • The group of Olivier Berteau from the ProbiHote laboratory (Interaction of commensal and probiotic bacteria with the host)
  • The Phenos platform which has been created to allow high throughput screenings of metagenomic clones
  • Partner 2 : INSERM U989 at the Medical Faculty René Descartes (Necker-Enfants-Malades), Paris. The Laboratory is headed by Nadine Cerf-Bensussan.
  • Partner 3 :  INSERM U872 (team7, Nutriomic), at the Research Center of Les Cordeliers, Paris. The team is leaded by Karine Clément.

Project Objectives

We have demonstrated that our new and innovative functional metagenomic approach was efficient in identifying genes potentially involved in host microbiota cross-talk in a high throughput manner (Lakhdari et al, PLoS one, 2010).

The objectives of FunMetaGen are now to fully characterize the mechanisms of these interactions at the molecular level from both the microbiota and host sides. Moreover, we aim at demonstrating the in vivo relevance of the identified mechanisms, in mouse models but also in humans.

 The different steps are :

  • Identification of candidate metagenomic clones able to modulate key targets in intestinal epithelial cells (IEC). These targets will be transcription factors NF-kB, AP1, and PPARgamma and three other genes of interest considering the role of epithelial cells in the immuno-regulatory functions of IEC, namely the cytokines Thymic Stromal Lymphopoietin (TSLP) and Transforming Growth factor (TGF)-b and the enzyme Retinaldehyde dehydrogenase 1 (RALDH1).
  • The second step will be, on one hand the characterization of the ORFs involved in the effect on IEC after sequencing and transposon mutagenesis, and on the other hand the deep characterization of the IEC transcriptomic responses to the metagenomic clones
  • The third step will be to decipher the mechanisms of the host microbiota interplay.
  • The last step is to analyse in vivo the patho-physiological consequences of the interactions both in mouse models and Humans.

Task 1        Project Management     List of deliverable


Website developed

Mo 3


Scientific Progress Report 1

Mo 6


Scientific Progress Report 2 and Financial Report

Mo 12


Copy of Consortium Agreement

Mo 12


Midterm Scientific Progress Report 3

Mo 18


Scientific Progress Report 4 and Financial Report

Mo 24


Scientific Progress Report 5

Mo 30


Final Scientific Progress Report  and Financial Report

Mo 36


Rolling Updates

  • Project Plan A meeting with all partners has been held on June 5th from 10 am to 1 pm at CRJ. Each partner presented his/her advances on the project.A very ...
    Posted Jul 30, 2013, 2:09 AM by Herve Blottiere
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