Focus on Microbial Ecology Modelling at the NEM days meeting in Rennes

Published: May 6, 2025 by FME Lab

The French NEM (Nutrition & Microbial Ecosystems) network hold its annual meeting this last two days (5th – 6th of May) in Rennes. Julien Tap, researcher from the FME lab presented the first results of his Ferment du Future SynthPlex project and how Engineering food microbial consortia can be performed using microfermentors to reveal strain epistasis. With the Support of Holoflux and Digit-Bio INRAE Metaprogram, He also co-organized with Guillaume Gautreau from the MaIAge Unit a specific workshop on modelling of microbial ecosystems.

In this session, Bastien Renard and Ayité Adama-Hondegla, PhD students involved in the #DominoEU project, presented their pioneering work in the design of microbial consortia for plant-based fermented foods using genome-scale modelling. The session resumed with additional strategies and perspectives presented by Maxime Lecomte (INRAE, STLO) and Daniel-Rios Garza (INRAE, Prose). Altogether, they showed that despite the promises that GSM can bring, many challenges remains to be overcome. A very interesting scientific field to follow in the near future.

During NEM days, Microbiome Modelization specific sessions program was:

Bastien Renard: Design of microbial solutions for healthy and sustainable innovative fermented cereal beverages
Ayite Adama-Hondegla: Microbial community assembly and metabolic diversity in a legume-based matrix
Maxime Lecomte: Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling
Daniel-Rios Garza: Towards the Development of Closed-Loop Microbiome Controllers

New tool suite - Food Microbiome Metabolic Modules (F3M)

The FME team has published a new preprint in Open Research Europe entitled
“Food Microbiome Metabolic Modules (F3M): a tool suite for functional profiling of food microbiomes.”
Read the article

A successful outcome of the EMOVOL project

The EMOVOL project has come to an successful end: a fruitful collaboration between INRAE and Fleury Michon has led to the development of a method for characterizing the preservation potential of cooked poultry meat products based on microbial biomarkers in raw meat.

A seed meeting between INRAE Micalis Institute and Imperial College London

Last week on October 3rd, scientists from Imperial College London (ICL) and from INRAE Micalis Institute were hosted by the French embassy in London for a seed meeting around synthetic biology and synthetic microbial ecology as scientific strategies for biotechnology and food production. A special thanks to the organizer: Ludovic Drouin (French Embassy), Young-Kyoung Park (Micalis) and Rodriguo Ledesma-Amaro (ICL). Our several groups with complementary research discussed about perspectives of future collaborations on the field together with Ferment du Futur or Bezos Centre.