A transition towards sustainable food systems is urgently needed to face challenges such as climate change or scarcity of resources. Food impact accounts for 26% of global greenhouse gas emissions. Animal-based food products in the European diet is the most important factor determining the footprint of food consumption. Plant-based dairy and meat alternatives have grown in popularity in recent years for various reasons, including sustainability and health benefits as well as lifestyle trends and dietary restrictions. However, plant-based food products can be nutritionally unbalanced, and their flavour profiles may limit their acceptance by consumers. Microorganisms have been used in making food products for millennia. Besides their primary role in food preservation, by virtue of their fermentative metabolism, they contribute to improving food safety and organoleptic properties and can provide additional health-promoting effects. However, the diversity of microbial communities driving plant-based fermentations, as well as their key genetic and phenotypic traits and potential synergies among community members, remain poorly characterized. Many data exist but they are spread into different literatures (scientific and grey) or in best case in different databases, but not always reusable because difficult to find, access and because databases are not systematically interoperable. The FAIN miss innovative interdisciplinary research programme will gather universities and private companies to enable the FAIRification of omics data and databases interoperability, and develop knowledge graphs for data-driven decision making to rationally design microbial communities for imparting desirable characteristics to plant-based fermented foods in the context of open science and its regulations. The FAIROmics training programme aims at developing Doctoral candidates' skills at the interface between artificial intelligence, life sciences, humanities and social sciences.