HoloRuminant will expand our understanding of ruminant-associated microbiomes to fill knowledge gaps and develop tools for their interpretation. With its holistic multi-omics approach, the project will study the multiple interactions of the ruminant-associated microbiomes with the host animal in early life and throughout fundamental life events. The aim is to decipher the characteristics and functions of livestock microbial ecosystems from different body sites, their heritability and their influence on the host’s resistance to disease and environmental efficiency of production (e.g., efficiency, disease resistance and resilience to changing environmental conditions). 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 sustainability.