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) ↩

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

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

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.

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 ↩