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Agrifood systems play a crucial role in numerous economic sectors, health and the environment. Faced with constant growth in global demand, these systems need to respond to numerous challenges in terms of health, well-being and sustainable development. The evolution of dietary behaviours, the emergence of new production modes and products and a marked increase in the prevalence of chronic diseases (metabolic diseases, allergies and intolerance, etc.) pose the question of food as a vector for health and well-being. Thus the phrase “we are what we eat” is increasingly being reflected in society, as testified by the boom in organic products, the growing distrust of consumers towards processed products and the adoption of foods deemed healthier and of better nutritional quality.

From field to fork, agrifood systems form a complex network that includes a wide variety of holobionts (vegetables, arable crops, fruit trees, farmed livestock, producers, farmers, consumers, etc.) and ecosystems (livestock units, cheese-makers, fields, etc.). This assembly of microbial communities remains permeable and dynamic under the action of the microbial fluxes passing between them. To respond to the societal demands mentioned above, the metaprogramme is trying to study both holobionts and microbial fluxes within agrifood systems, including the management of micro-organisms within them. It focuses in particular on the challenges of sustainable foods (performance and efficiency of the food system, short channels, reducing greenhouse gas emissions, maintaining biodiversity, etc.) and preserving the health of plants, animals and humans (reducing inputs, antibiotics and pesticides, using microbiotas to combat pathogens, etc.).

Programming areas

Area 1: Mechanisms underlying assembly and interactions within holobionts

Study of holobionts whether they concern plants (plants, trees), animals (insects, pests, livestock) or humans. Understanding the principles underpinning their assembly throughout life cycles constitutes a valuable source of information for resource management. The issues addressed are common to different holobionts displaying particular characteristics and thus a certain complementarity.

Area 2: Microbial flux and dynamics within an agrifood system

Within agri-food systems, holobionts are subject to the influence of numerous biotic and abiotic disturbances.  This area of research concerns the study of the effect of microbial flux on holobionts, the impact of different production systems (conventional or alternative) on an agri-food system, and the identification of critical stages for sustainability throughout this system.

Area 3: Control and management of microbial fluxes and their impact on performance, sustainability and health

Host-microbiota interactions involve and are influenced by three actors: the microbiota, the host and the environment. Each of these three levels offers opportunities to control and steer the other actors.