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) ↩

The FME lab communicates about the links between the microbiome, nutrition and health.

On Thursday 27 November, the FME lab took part in the Food System Microbiomes Conference in Wageningen during the session dedicated to the connections between microbiomes, nutrition and health. The session was co-chaired by Stéphane Chaillou (INRAE, Micalis) and Prof. Christophe Courtin (KU Leuven), and provided an opportunity to showcase advances from two major European projects: DOMINO and HealthFerm.

Understanding How Fermented Foods Shape Health Insights From a New PIMENTO Review

A new scoping review published in Frontiers in Nutrition¹ as part of the COST Action PIMENTO initiative provides a comprehensive assessment of what is currently known about the health effects of fermented foods in specific human populations. This work reflects a substantial collective effort. We conducted an extensive and rigorous screening of the scientific literature, reviewing and selecting studies across many categories of fermented foods and health outcomes.

Humblot Christèle, Alvanoudi Panagiota, Alves Emilia, Assunçao Ricardo, Belovic Miona, Bulmus-Tuccar Tugce, Chassard Christophe, Derrien Muriel, Karagöz Mustafa Fevzi, Karakaya Sibel, Laranjo Marta, Mantzouridou Fani Th, Rosado Catarina, Pracer Smilja, Saar Helen, Tap Julien, Treven Primož, Vergères Guy, Pertziger Eugenia, Savary-Auzeloux Isabelle, A scoping review of the health effects of fermented foods in specific human populations and their potential role in precision nutrition: current knowledge and gaps. Frontiers in Nutrition. 2025 doi:10.3389/fnut.2025.1650633 ↩

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.”
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