Objective 1 investigates the fruit microbiome in Agroscope trials, assessing microbial dynamics under storage protocols and biocontrol treatments. We progress from individual strains to synthetic communities (syncoms) to design complex biocontrol systems against postharvest losses. Long-read nanopore metabarcoding and metagenomics will deepen analysis. A major focus is Neofabraea spp., integrating genomic and transcriptomic profiling, host susceptibility, and epidemiology. Novel food matrices are also explored.

Objective 2 targets microbiomes in food fermentation and spoilage, providing diagnostics for apple juice producers and applying nanopore sequencing to spoilage studies. We track microbial dynamics in wine production from disease-resistant grapes, testing microbiome management strategies and linking them to sensory outcomes, with collaborations on Swiss spirits optimization.

Objective 3 examines microbiome transmission from produce to the human body, comparing produce and oral swabs to reveal transmission routes and oral health impacts. A ribosomal sequence database and antibiotic resistance investigations extend our scope “from farm to fork” toward “farm to body.”