Over the past decade, program research has become one of the cornerstones of Agroscope research. It enables to specifically promote agricultural research topics that were identified as highly relevant, that are innovative, interdisciplinary, and importantly, that further collaboration among different Agroscope research groups as well as with external researchers. The selection process for ARPs is highly competitive and requires acquisition of matching third-party funds. The ARP Microbial Biodiversity was initiated by Elisabeth Eugster and Barbara Guggenbühl, then of the research group “Cultures, Biodiversity and Terroir” at Agroscope Liebefeld-Posieux ALP in Liebefeld. The overarching aim of this ARP is to identify and eventually further, utilize and apply possible beneficial effects of specific microbial communities for improved and sustainable agricultural and food production. This is to be achieved by studying and describing microbiomes, i.e. the totality of microorganisms in an ecosystem, as well as the functions of the most important players in three ecosystems that are highly relevant for the agriculture and food sector: soil, plant, and fermented dairy products. These three ecosystems are studied in three Work Packages (WP). WP 1 deals with the soil microbiome, with its manifold functions in agriculture. WP 2 analyses the plant microbiome, with a main aim to identify microorganisms, which have a favorable influence on important crop plants, and which may contribute to reduce pathogen infestation. WP 3 analyses the microbiomes of fermented dairy products, which are important Swiss agricultural commodities. A fourth WP involves the setting up of an Agroscope-wide expert network in genomics and bioinformatics and the corresponding infrastructure. The aim is to develop and apply state of the art methods to describe microbiomes and to functionally characterize relevant strains using functional genomics approaches. These core competences are applied in interdisciplinary collaboration with the ARP and beyond. During the past four years, technologies and methods have been implemented and developed in Agroscope projects and fundamental knowledge has been built that will promote and direct Agroscope research activities into the future.