Sustainability of ruminant production is of concern to society because of its implications for the environment, the economy and food security. Microbiomes associated with the host play a key role in health, welfare and environmental efficiency in ruminant production systems. However, despite the information already available, we lack the insights to precisely link the causes and mechanisms of microbial influence on ruminant phenotypes. This is because the interconnection and communication between the animal and its different microbiomes have never been studied in a deep, integrated way. The goal of the project is to elucidate the role of ruminant-associated microbiomes and their interplay with the host in early life and throughout fundamental life events. HoloRuminant will use a holistic multi-omics approach to characterise the acquisition and evolution of microbiomes from different body sites, their inheritability and their influence on the host’s resistance to disease and environmental efficiency of production. Specifically we will: determine microbiomes’ functions by combining multi-level information for microbes, host and their interaction; define microbiomes’ roles during challenging life periods such as perinatal, weaning, and after exposure to pathogens; and evaluate the effect of ruminant microbiomes on critical phenotypes for sustainable production, health and welfare. This will allow the identification of novel microbial markers for monitoring, predicting and selecting phenotypes of interest. By engaging actors from the livestock value chain, we will evaluate the socio-economic impact and acceptability of the innovations proposed among stakeholders and the public. HoloRuminant will provide highly innovative, standardized methodologies that will radically advance our understanding of the ruminant holobiont. This knowledge and the tools created will allow the use of microbiome-based diagnostics and solutions for improving ruminant sustainabilty.