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FAIRification of multiOmics data to link databases and create knowledge graphs for fermented foods

Project description

Knowledge graphs to characterise plant-based fermentations

Plant-based dairy and meat alternatives are gaining popularity. However, they can be nutritionally unbalanced, and they require better taste profiles. Microorganisms have been used for millennia in food production, preservation and safety improvement. Nevertheless, the intricate microbial communities steering plant-based fermentations need better characterisation, as data is scattered across various sources. The MSCA-funded FAIROmics project aims to establish an interdisciplinary research programme for the FAIRification of omics data and database interoperability. This initiative also seeks to develop knowledge graphs to facilitate data-driven decision-making and design microbial communities for plant-based fermented foods. Additionally, the project includes a training programme to enhance the skills of doctoral candidates in AI, life sciences, humanities and social sciences.


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 FAIROmics 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.


Net EU contribution
€ 565 387,20
75007 Paris

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Ile-de-France Ile-de-France Paris
Activity type
Research Organisations
Total cost
No data

Participants (10)

Partners (16)