HoloRuminant is a five-year project organized around five research work packages (WPs), supported by one WP in charge of dissemination and communication (WP6) and one WP in charge of project coordination and management (WP7). Existing knowledge on ruminant microbiomes will be consolidated, expanded with new data and the development of analytical tools and stored in an integrated open access database (HoloR, WP1). The project will run longitudinal studies to generate knowledge on the establishment and colonization of multi-site microbiomes over time and their impact on health and productivity of ruminants (WP2) and intervention studies on the effect of these microbiomes on specific phenotypes related to health and environmental issues covering different species, management systems, diets and environments (WP3). The knowledge generated at different omics levels (WP2 and WP3) will be stored in the HoloR database (WP1) and used to understand how the interactions between specific microbiomes and environmental parameters can be connected to the host variance and, ultimately, exploited to improve KPIs of ruminants (WP4). The tools (including software, bioinformatics pipelines, diagnostics, beneficial microbes, integrated microbiome network information, etc.) developed from this knowledge will be openly available (HoloR-tools, WP4, WP1). The economic feasibility of the innovations proposed will be modelled for farmers and industry, whereas social views and acceptance will be evaluated using participatory methods and consultation with stakeholders throughout the project (WP5).