Many studies support the role of beneficial microbiomes for improving agri-food production and human health. Only during the last decade, we have begun to gain insights into the composition and functional of microbiomes as a consequence of major advances in High Throughput DNA sequencing (HTS) technologies. Microbiomes occupy a central position in the “One Health” framework. They can colonize almost all biological niches including plants and humans providing benefits to the planet as a whole and everything that lives on and in it. Plant-associated bacteria can be found in fact on leaves, roots or in the internal tissues as well as human-associated bacteria can reside on or within human. The application of beneficial microbes into agriculture can contribute to providing healthy food in a sustainable manner by reducing the amount of fertilizer, pesticides and herbicides. Given the food link, microbes from vegetable-diet can also have a direct and indirect effects on human health. In this special Issue, we kindly invite the research community to submit original research papers and reviews that provide newest insights into the structure and dynamics of the core microbiomes across the food system (from soil to plants, and from foods to human) and to better investigate how we can use or manipulate microbiomes for achieving enhanced crop production and/or improving human health.

Keywords: Plant Growth-Promoting Microorganisms; Probiotics; Sustainable agriculture; Food system; Plant-food microbiome; Gut microbiome; Host-microbe interaction; Human health; Dysbiosis; Heathy diet