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

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.

School of Artificial Intelligence Applied to Microbiomes

Earlier this month, Julien had the pleasure of participating as a lecturer at the School of Artificial Intelligence Applied to Microbiomes, hosted at AgroParisTech and organized by Aristeidis Litos, Daniel Garza, and Ariane Bize. The event brought together an exceptional group of researchers and students exploring how AI, data science, and mathematical modeling are reshaping our understanding of microbial ecosystems.

Consumers at the core of fermented food innovation

Yesterday on September 23rd, about 100 participants from academia, industry, NGOs and policy makers across Europe had joined the second Stakeholder Forum of Horizon Europe #DominoEU project. Four speakers Pr. Jutta Roosen from the Technical Universty of Munich, Dr. Emmanuella Magriplis associate professor from the Agricultural University of Athens, Dr. Michail Syrpas associate professor at Kaunas University of Technology in Lithuania and Dr. Nikoletta Vidra Science Manager at Yakult Europe altogether spotlighted the central role of consumer research in advancing the field of fermented foods.