From food spontaneous fermentations to food designed consortia

Published: Dec 8, 2025 by FME Lab

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.

This review focuses on community-level genome or metagenome-scale metabolic modeling as a strategy to rationalize and predict microbial interactions in food. We underline its power as a cornerstone in comprehensive and rational strategies for optimization of microbial consortia assembly, whether they are used in bottom-up or top-down approaches.

A specific thanks to Elham Karimi, postdoc in the FME lab, who brought this discipline into the scope of our research group and which we now apply in many of our projects, including in the ANR metasimfood project and the European #DominoEU project.

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 ↩

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 ↩