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 ↩

HoloGen symposium on microbial meta-community modeling

On October 21, 2026, Julien Tap participated as an invited speaker in the Microbial Meta-Community Modeling symposium, organized by Karoline Faust at the Rega Institute, KU Leuven, Belgium, as part of the HoloGen doctoral network retreat.

Fermented foods at the Fête de la science Paris-Saclay 2026

On October 3–4, 2026, Stéphane Chaillou and Alice Lima took part in the Village des sciences at ENS Paris-Saclay for the Fête de la science, France’s annual science festival. This year’s theme, “Saveurs savantes”, invited visitors to explore the science behind food and flavour.

From “synthetic” to defined microbial communities for clearer terminology

Stéphane Chaillou participated in a joint reflection with a group of international researchers, coordinated by the Austrian Institute of Technology (AIT), on the terminology used to describe certain microbial communities. The collective of experts proposes replacing the term “synthetic community” (or SynCom), sometimes perceived negatively, with “Defined Microbial Community”.