School of Artificial Intelligence Applied to Microbiomes

Published: Oct 1, 2025 by FME Lab

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.

In his lecture¹, Julien discussed how large-scale metagenomic datasets—integrating taxonomic, functional, clinical, and nutritional dimensions—can help bridge high-dimensional data with ecological meaning. By examining tens of thousands of gut microbiome samples, we can uncover branching ecological states that describe how lifestyle, diet, and physiology shape microbial diversity. These ecological transitions not only reflect resilience and degradation dynamics but also offer a foundation for precision nutrition and the design of next-generation fermented foods.

A warm thank you to the organizers, speakers, and participants. It’s exciting to see how this field continues to grow, blending theory, computation, and experimentation toward a deeper understanding of microbiomes.

Julien Tap. Integrating Human Gut Microbiome Data at Scale: From Individuals to Multi-Layered Features in Clinical and Nutritional Studies. School of Artificial Intelligence Applied to Microbiomes: data analysis, modelling, and engineering of microbiome-based biotechnologies, Université Paris-Saclay, Oct 2025, Palaiseau, France. (hal-05312010) ↩

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

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.