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 ↩

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 ↩