Insights from Metabolomics and Fermented Foods 2024

Published: Feb 29, 2024 by FME Lab

The recent ‘Metabolomics and Fermented Foods’ seminar organized by the Netherland Metabolomic Centre and held at the Danone Nutricia Global Research & Innovation Center in Utrecht was a melting pot of groundbreaking ideas and discussions, delving deep into the intricate relationship between metabolomics, fermented foods, and gut health. Esteemed experts like Paul Cotter, Guus Roeselers, Barbara Koroušić Seljak, and others shared their invaluable insights, providing attendees with a comprehensive understanding of this dynamic field.

Julien shed light on the critical role of the gut microbiome in human health. He emphasized that while diet and lifestyle are significant, the resilience of the microbiome is pivotal in maintaining its structure over a person’s lifetime. His research, involving the analysis of 35,000 human gut microbiome samples, revealed that the microbiome operates in a branching structure, influencing the dynamic interplay between different states.

Julien underscore how effect fermented foods in promoting gut health might depend on gut microbiome states. In addition, using preliminary data from SynthPlex and MetaSimFood, he showed that the interaction between the strains in fermented foods and the metabolites in the food matrix is complex, suggesting that the potential benefits of fermented foods require further exploration.

Slides from Julien’s talk are available here: https://hal.inrae.fr/hal-04489205

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 ↩

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.