As the world population is continuously increasing, the supply of food with equal accessibility has become a major issue and future challenge. Microbes are unexploited tool to increase food productivity and quality. The objective of SIMBA project is to harness complex soil and marine microbial communities (microbiomes) for the sustainable production of food. SIMBA will focus on two interconnected food chains, i.e. crop production, aquaculture. SIMBA will first launch an in silico phase in order to analyze the further pre-existing microbiome databases and earlier studies, to identify the best microbiome layout capable of supporting food chain quality and productivity. Microbiome-tailored interventions will be specifically developed including soil, plant, fish, aquaculture and food/feed processing towards optimal layout as defined in the modelling step, as follows: i) Identified optimal microbiome consortia will be designed and tested in lab, pot and field trials to improve plant productivity and health; ii) Marine microbiomes will be applied to facilitate sustainable aqua and agriculture; iii) Optimal microbe/microbe consortia will be used to convert raw-materials and residuals to high quality food, feed or finally to energy. In a final intervention step, these interactions will be monitored and tested in field, aqua-culturing, fish feeding and human studies, measuring the impact on microbiome consortia, interactions in association with factors evaluating their efficacy in terms of improving food security, productivity, quality, safety, sustainability, nutritional and health aspects. "Near to market” microbiome applications for sustainable food systems will be provided thanks to the interdisciplinary and cross-sectional nature of the proposal and the active role of small and medium sized enterprises (SMEs).