Up to 80 % of all bacterial and archaeal cells across the world live in microbial aggregates. Engineered aggregates or biofilms, have become a crucial part of energy recovery and waste management technologies, such as anaerobic digestion facilities (conversion of waste to biogas). Upon encountering stress, biofilms actively expel distinct microorganisms. This mechanism could offer great potential for anticipating and preventing functional biomass wash-out. To achieve a deeper understanding of how this dispersal works and what these expelled microorganisms distinct features are, I will study their observable (phenotypic) properties in this project proposal. First, I will focus on anaerobic granules as a model microbial aggregate. By integrating phenotypic information acquired through flow cytometry with transcriptomic and proteomic information, a dispersal fingerprint will be obtained. Next, I will investigate if this dispersal fingerprint can be used as an early-warning monitoring tool for bio-engineered systems. Finally, the dispersal fingerprint of different biofilms from various ecosystems will be compared, thus, providing a detailed understanding of how phenotypic and genotypic dispersal properties are related across different biofilms. Ultimately, this knowledge will enable the implementation of flow cytometry-based monitoring tools as fast, cost-efficient tools for managing bio-engineered ecosystems by steering them towards microbial stability.