Workshop on FAIR omics data in the M4SF cluster of European HE projects

Published: May 17, 2024 by FME Lab

Last Friday 17th of May, in the frame of the 1st Food System Conference in Torino , Stéphane Chaillou organized the second clustering activity of the #Microbes4SustainableFoods cluster of EU projects (#DominoEU, #HealthFerm, #Pimento ca20128, #Wheatbiome, #Tribiome and #Microbes) on the Friday afternoon after the conference closure.

FAIR and standardised omics data generation, use and storage of these data at the research level and join activities on this topic between the various projects was at the heart of the discussion. Within the next four years, various omics data (metagenomics, metatranscriptomics and metabolomics) will be produced on thousand of plant-based fermented food samples and on several soil microbiomes such as wheat and olives. The cluster will work to ensure that this deluge of omics data will comply to FAIR principles, with a specific focus on metadata agreements, in order to increase the interoperability of these data among the various databases that will be produced. This very fruitful discussion will help starting joined efforts between the projects.

A special thank you to the participants: Fani Mantzouridou (AUTH), Jekatarina Kazantseva (TFTAK), Hélène Chiapello and Julien Tap (INRAE), Dominique Swennen (INRAE, coordinator of FAIRomics doctoral network), Tony Burdett (EMBL-EBI), Cristina Varese, Marco Beccuti (SUS-MIRRI-IT project), Luca cocolin, Kelly Rantsiou and Ilario Ferocino (UNITO), Enrique Cubas-Cano (ITENE).

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(#DominoEU researchers participated significantly to this amazing conference organised by the COST Pimento. Paul Cotter, Orla O’Sullivan, Jekaterina Kansatseva, Bastien Renard, Isabelle Savary-Auzeloux, Luca Cocolin, Kelly Rantsiou and Tanja Kostic gave talks.

Metagenomic driven isolation of poorly culturable species in food

A new article entitled “Metagenomic driven isolation of poorly culturable species in food” from Caroline and Pierre has been published in Food microbiology journal¹.

Kothe et al. *Metagenomic driven isolation of poorly culturable species in food. Food Microbiology. 2025 ↩

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On Tuesday 7th of January, the 7 partners gathered for the second time in Illkirch (close to Strasbourg) and were hosted by Aérial. The meeting was focused on the main advances carried out on the fermented vegetables food model with exiting results confirming the hypothesis postulated earlier in the project. Also, the evening before the meeting, Aérial organized a specific visit of the largest Sauerkraut producer in France, at a small village 30 km south of Strasbourg.