Webinar on genome-scale modelling for consortia design

Published: May 28, 2024 by FME Lab

Last Tuesday 28th of May, Elham Karimi, Stephane Chaillou (Micalis, Food Microbial Ecology research group) and Valentin Loux (MaIAge) have organised in the frame of the #DominoEU project a webinar training session on genome-scale modelling (GSM).

This training aimed at performing the first cross-capacity building between two workpackages (WP3: Open access databases & computational tools) and (WP4: design of microbial consortia for sustainable plant-based fermented foods) and towards scientists from various background. GSM will be used in #DominoEU project for the design of microbial solution for various plant-based fermented food. Metagenomic and genomic data from samples and strains isolated at the beginning of the project will be used as template for this very challenging but exciting modelling. Next steps will be the GSM workshop 24-26th of June in INRAE Jouy-en-Josas.

Special thanks to the participants: Pascal Bonnarme, Vincent Hervé, Ayité Adama, Sophie Schbath (INRAE) ; Ilaria Ferrocino, Kelly Rantsiou (UNITO) ; Abelardo Margolles, Pedro Riesco, Lorena Ruiz (CSIC) ; Bastien Renard, Christèle Humblot (IRD) ; John Kenny, Katie O’Mahony, Anik Khan (TEAGASC) ; Jekaterina Kazantseva (TFAK) ; Claudia Mengoni, Hriturak Dey (UNITN) ; Tanja Kostic (AIT).

FME at Bioket 2026 advancing synthetic microbial ecology for sustainable food

At the BIOKET (Bioeconomy Key Enabling Technologies) conference in Fribourg, Julien presented recent advances from the SynthPlex project, positioning synthetic microbial ecology as a core tool for next-generation fermented foods.

cFMD workshop in Trento

Last February 23-24th 2026, at University of Trento, a workshop was organized by the CIBIO (Nicola Segata’s lab) for #DominoEU partners. The workshop aimed at learning to query & analyse data from the Curated Food Microbiome Database (cFMD). Thanks to the very efficient and skilled teaching team (vitor Heidrich, Hrituraj Dey, Francesco aniscar, Sergio Andrés Castañeda Garzon) and for the incredible hospitality of Frederica Pinto and Nicola Segata.

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 ↩