The concept of a multicellular organism to describe complex organisms composed of groups of analogous cells called tissues and organs with specific functions, shows currently some limitations. An organism such as a plant does not live alone, but closely associated with different microbial communities making up its microbiomes. The microbiomes, specific to a tissue, interact with the plant and modulate some of its functions, including physiology and immunity. The host and the associated microbiomes define a holobiont, whose function is influenced by the spatio-temporal dynamics of their interactions. Thus, a dysfunction of the grapevine holobiont (linked for example to inappropriate technical itineraries or to climate change) could lead to the development of diseases or physiological disorders, similarly to the alteration of gut microbiota observed in numerous human diseases as type 2 diabetes, obesity and irritable bowel syndrome. The analysis of microbial communities associated with a plant such as grapevine has until recently been limited by the fact that most microorganisms cannot be cultured in vitro. New methods (named -omics) based on the analysis of genome, metabolome and proteome allow to define the taxonomic and functional characteristics of the different microbiomes associated with a plant, in particular organisms (i.e. bacteria, fungi) that are not cultivable. In the Holoviti project, we aim to characterize the role of microbiomes in grapevine homeostasis by describing and comparing the holobiont of i) healthy grapevines and ii) grapevines affected by three declines (Esca / BDA, fanleaf and linked to 161-49C rootstock). One of our objectives is to identify taxonomic and functional bio-indicators (linked to either microbes or the plant) of the host sanitary status. One prospect could be handle the microbial component of the holobiont to improve some ecosystemic services, such as the control of pathogens or the fight against abiotic stresses.