Holobionts and microbial flux within agri-food systems

December 03, 2020

Organized in collaboration with





  • Emmanuelle Maguin (Holoflux Program Directorate, INRAE, FR)
  • Manuel Blouin (Agroecology unit, INRAE, FR)
  • Claire Rogel-Gaillard (Animal Genetics and Integrative Biology unit, INRAE, FR)


A holobiont is a host (plant, animal or human) and its associated microbial communities (bacteria, viruses, archaea, protists and microscopic fungi). A recent paradigm shift proposes that individual phenotypes result not only from the expression of the host genome, but also from the combined expression of the host and associated microbial genomes. Moreover, holobionts are rarely isolated in the environment and are continuously submitted to microbial flux that can disturb the assembly and the stability of the microbial communities involved. Thus, studying holobionts and microbial flux is of crucial interest in many different ecosystems, and particularly in agrifood systems. In this webinar, we will first present the research challenges that needs to be addressed by the scientific community in order to set the ground toward the control and use of holobionts as levers for improving performance and sustainability of food systems while preserving human, animal and plant health:

  1. Mechanisms underlying assembly and interactions within holobionts
  2. Microbial flux and dynamics within an agrifood system
  3. Control and management of microbial fluxes and how they impact performance, sustainability and health

INRAE promotes the development of integrated projects using systemic and interdisciplinary approaches in order to examine several components of a complex system and their interconnections.

We will present two examples of exploratory research projects running at INRAE on different types of holobionts within agrifood systems:

  • the HOUSE project : “Microbial communities in the rhizosphere: a selection unit?”
  • the ENTEROTYPIG project “Enterotypes of the intestinal microbiota in pigs: characterisation and influence of the host genetics to assemble the holobiont