Although microorganisms dominate almost every ecological niche in our planet, it has only been during the past 10-15 years that we have begun to gain insights into the composition and function of microbial communities (microbiomes) as a consequence of major advances in High Throughput DNA sequencing (HTS) technologies. These approaches have allowed a comprehensive analysis of microbiomes for the first time. Following initial curiosity-driven investigations of microbiomes using HTS technologies, the field has evolved to harness the insights provided, leading to the development of a new multi-billion euro industry focused on characterisation and modulation of microbiomes. The vast majority of this investment has been in the clinical space. In contrast, far less is known about microbiomes across complex food chains, making it difficult to harness food-chain microbiome data for the development of more sustainable food systems and to yield innovative products and applications. This is despite the evident importance of microbes throughout the food chain. MASTER will take a global approach to the development of concrete microbiome products, foods/feeds, services or processes with high commercial potential, which will benefit society through improving the quantity, quality and safety of food, across multiple food chains, to include marine, plant, soil, rumen, meat, brewing, vegetable waste, and fermented foods. This will be achieved through mining microbiome data relating to the food chain, developing big data management tools to identify inter-relations between microbiomes across food chains, and generating applications which promote sustainability, circularity and contribute to waste management and climate change mitigation. We will harness microbiome knowledge to significantly enhance the health and resilience of fish, plants, soil, animals and humans, improve professional skills and competencies, and support the creation of new jobs in the food sector and bioeconomy.