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

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”.

Harnessing gut microbiome diversity for next-generation fermented foods

On June 5, 2026, Julien Tap participated in the INRAE-Tokyo NODAI Joint Symposium on Fermentation and Food Bioscience. This online event brought together researchers from INRAE and the Tokyo University of Agriculture to discuss fermentation microbiology, food bioscience, taste, and microbiome-based approaches to health. More than 100 participants attended the symposium, most of them Japanese students, highlighting the strong interest of the next generation in fermentation and microbiome science.

DOMINO 3rd annual meeting in Madrid

After three years, the #DominoEU project has reached full speed, with significant results across all project objectives. The three-day meeting provided an opportunity to review the very busy year of 2025 and the many key findings that can be leveraged in the coming months.