Holoruminant is a multi-actor project aiming to elucidate the role of ruminant-associated microbiomes and their interplay with the host animal in early life and throughout fundamental life events (e.g. weaning, feed transitions and lactation) that are known to affect health, welfare and environmental efficiency in ruminant production systems. HoloRuminant will use a holistic multi-omics approach to characterize the establishment and dynamics of microbiomes. In this way, HoloRuminant will determine the connectivity between microbiomes from different body sites, their heritability and their influence on the host’s key performance indices (KPIs) of efficiency of production, growth, resistance to disease, methane emissions, carbon footprint and phenotypic resilience to changing environmental conditions. The main outputs of the project will be the creation of an expandable benchmark dataset of ruminant-associated microbes, microbiomes and methods for analysis that will be used for answering essential (who, what, where and when) scientific questions and will be the knowledge foundation for innovation.