News

from FME lab

Subscribe
Food microbial fluxes under the magnifying glass of multi-omic data integration
Food microbial fluxes under the magnifying glass of multi-omic data integration

In our last article1 published online this Wednesday 18th of October in frontiers in Microbiology, we demonstrate how an ambitious meta-omics sampling strategy can be holistically integrated to reveal the secrets of microbial flux within food production. Our paper focuses on spoilage scenarios in meat products, but the concept can be applied broadly to all types of food. We demonstrate that, in addition to studying the parameters influencing microbial flux, it is also possible to highlight certain metabolic interactions between micro-organisms. Many thanks to the ANR for funding this project, and a wave of congratulations to all our colleagues in this consortium.

  1. Poirier, S. et al. Holistic integration of omics data reveals the drivers that shape the ecology of microbial meat spoilage scenarios. Front. Microbiol. 14, 1286661 (2023). 

Bringing synthetic Ecology in the field of food microbiology
Bringing synthetic Ecology in the field of food microbiology

The 18th national congress for the French Microbiology Society (SFM) was held in Rennes the 4-6th October. Stéphane was welcome as a guest and gave an introduction conference in the session dedicated to “microbes and functional foods”. He delivered a 25 min talk untitled ”Design of microbial solutions for sustainable and healthy fermented food: perspectives & challenges”.

Ferment'IA: Bridging the World of Fermented Foods with Artificial Intelligence
Ferment'IA: Bridging the World of Fermented Foods with Artificial Intelligence

On the 13th of September, CentraleSupélec hosted the inaugural Ferment’IA colloquium. This event, organized in collaboration with Ferments du Futur and l’Institut DATAIA, catered to researchers focusing on Artificial Intelligence (AI) and Data Science, particularly in the context of fermented foods.

A Glimpse into LAB14: Insights on the Future of Lactic Acid Bacteria science
A Glimpse into LAB14: Insights on the Future of Lactic Acid Bacteria science

The 14th Symposium of Lactic Acid Bacteria (LAB14) in Egmond aan Zee, Netherlands, was a landmark event in the world of microbial ecology. Renowned experts from across the globe congregated to discuss the latest advancements in the field.

Third scientific meeting of ANR metasimfood project in Palaiseau
Third scientific meeting of ANR metasimfood project in Palaiseau

The meeting was organised by sayfood partner in the brand new AgroParisTech building in Palaiseau. These two days were focussed on the milestone around the construction of the food models and construction of artificial microbial communities. We are glad that this important milestone is validated. The project will now enter a more ambitious phase, implementing synthetic ecology strategies to model microbial interactions in the project’s two models (wine and fermented vegetables). The meeting was punctuated by a very pleasant dinner at the living-room in Palaiseau.

Latest Posts

FME at Bioket 2026 advancing synthetic microbial ecology for sustainable food
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
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
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.

  1. 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