DOMINO Workshop on genome-scale modelling. How to build innovative and forward-looking methodologies in the field of fermented foods

Published: Jun 6, 2024 by FME Lab

The last three days, from Monday 24th to Wednesday 26th of June, INRAE (MaiAge & MICALIS) teams organised a workshop on microbial community-level genome scale modelling (GSM) for consortia design.

This activity was organized by INRAE scientist from #DominoEU WP3 (dedicated to open food microbiome database and tools) for WP4 (Microbial consortia design for plan-based fermented foods) partners. It was also the opportunity to align methodologies developed in French ANR #Metasimfood project to those being developed in #DominoEU project.

A special thanks to Elham Karimi from Metasimfood project and her skill in the field which allowed a strong capacity building in Domino. Many thanks also to Valentin Loux for setting the bioinformatic framework of the Migale computational cluster.

Thanks to Katie Fala from Teagasc and Vitor Heidrich from University of Trento for ensuring, despite the rush, that both genomic and metagenomic data were released and annotated properly for the training. Results are very promising and GSM will go on in the coming weeks for further tuning of the models. Congratulations to the participants Katie Fala, Ilario ferrocino, Xenia Vasquez, Hindrek Teder, Vincent Hervé, Ayité Hadama, Julien Tap and Bastien Renard. Luckily, weather was perfect for casual lunch near the workshop room and for a charming terrace diner in Versailles at the restaurant “La Salamandre” on Tuesday.

From food spontaneous fermentations to food designed consortia

Our new article entitled “Microbiome metabolic modeling as a tool for innovation in fermented foods” has been published in in Current Opinion of Food Science¹.

Elham Karimi, Julien Tap, Marie-Christine Champomier-Vergès, Stéphane Chaillou. Microbiome metabolic modeling as a tool for innovation in fermented foods. Current Opinion of Food Science. 2025 ↩

The FME lab communicates about the links between the microbiome, nutrition and health.

On Thursday 27 November, the FME lab took part in the Food System Microbiomes Conference in Wageningen during the session dedicated to the connections between microbiomes, nutrition and health. The session was co-chaired by Stéphane Chaillou (INRAE, Micalis) and Prof. Christophe Courtin (KU Leuven), and provided an opportunity to showcase advances from two major European projects: DOMINO and HealthFerm.

Understanding How Fermented Foods Shape Health Insights From a New PIMENTO Review

A new scoping review published in Frontiers in Nutrition¹ as part of the COST Action PIMENTO initiative provides a comprehensive assessment of what is currently known about the health effects of fermented foods in specific human populations. This work reflects a substantial collective effort. We conducted an extensive and rigorous screening of the scientific literature, reviewing and selecting studies across many categories of fermented foods and health outcomes.

Humblot Christèle, Alvanoudi Panagiota, Alves Emilia, Assunçao Ricardo, Belovic Miona, Bulmus-Tuccar Tugce, Chassard Christophe, Derrien Muriel, Karagöz Mustafa Fevzi, Karakaya Sibel, Laranjo Marta, Mantzouridou Fani Th, Rosado Catarina, Pracer Smilja, Saar Helen, Tap Julien, Treven Primož, Vergères Guy, Pertziger Eugenia, Savary-Auzeloux Isabelle, A scoping review of the health effects of fermented foods in specific human populations and their potential role in precision nutrition: current knowledge and gaps. Frontiers in Nutrition. 2025 doi:10.3389/fnut.2025.1650633 ↩