The BeMyGuild project aims to move beyond siloed microbiome studies and establish a generalisable, guild-based framework for analysing microbiomes across connected ecosystems. The project is grounded in the hypothesis that despite significant taxonomic variation across environments, shared ecological and functional principles can be identified through guilds — groups of microorganisms whose coordinated activities facilitate quantifiable processes and results. The dairy value chain will be used as a model system by BeMyGuild to test this concept, since it offers a unique succession of physically and biologically connected compartments whose microbiomes influence animal health and production, environmental impacts and the properties of dairy products relevant to human health and nutrition. To this end, the project will integrate heterogeneous microbiome resources into a harmonised, FAIR-compliant backbone, combining computational guild inference with experimental reconstruction, as well as mechanistic and causal modelling and systems-level validation. The dynamics of guilds and their links to ecosystem processes will be investigated using longitudinal and multi- compartment experimental designs that combine microbiome profiling with metabolomic and targeted chemical signatures. By linking guilds to metabolic outputs, environmental conditions, and system-level responses, BeMyGuild will pave the way for the transition from descriptive microbiome profiling to mechanistic, causal, and predictive microbiome science. The project will also deliver harmonised workflows, metadata standards and deployable tools via European research infrastructures. The broader acceptability and sustainability of guild-based interventions will be assessed through multi-actor scenario development and life cycle approaches, providing decision-relevant indicators and supporting innovation pathways.