Microbial post-harvest diseases can be controlled using existing methods (synthetic fungicides, CA- Storage, 1-MCP). With the pressure of reducing synthetic fungicides (Swiss action plan in plant protection, EU- regulation), an increase of microbial post- harvest disease and thus an increase in food loss is to be expected. Using state of the art molecular methods (spore sampling, molecular diagnostic assays, metagenomics) microbial diseases can be characterized to a previously unknown resolution and the resulting information can be applied to obtain a high fruit quality with decreased input of synthetic plant protection products. Additionally, existing biocontrol methods (Aureobasidium, Metschnikowia) are evaluated and novel antagonists are identified. In order to characterize these pathogens, antagonists and complete microbiomes, state of the art technologies in molecular diagnostics (PCR, LAMP) and sequencing (Sequencing-by-synthesis, Nanopore) are evaluated and applied within the Swiss agricultural system. In order to assess the quality of fruits, methods in physical and chemical analytics are applied continuously and novel methods are evaluated.