New tool suite - Food Microbiome Metabolic Modules (F3M)

Published: Nov 6, 2025 by FME Lab

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.”
Read the article

Understanding microbial interactions within food ecosystems is essential for improving the quality, safety, and health properties of fermented foods. However, analyzing these interactions at the functional and metabolic levels remains technically challenging. To address this gap, the FME team developed F3M, an open-source suite designed specifically for the metatranscriptomic analysis of food microbiomes.

Overview of different classes among the F3M main functional modules allowing the linkage of the major functional processes in microbial interactions. — Overview of different classes among the F3M main functional modules allowing the linkage of the major functional processes in microbial interactions:: the modules for metabolism (illustrated by the pathways within the two bacterial cells), redox processes (central oxido-reduction mechanisms between the two cells), and uptake processes (various transporters in the cell membrane of the two cells).

The F3M suite includes:

A curated database of nearly 2,000 functional genes representing key fermentative reactions
The F3M Builder, a workflow for constructing annotated gene catalogs and mapping sequencing data
The f3mr R package, which enables aggregation and analysis of gene expression data across taxonomic and functional levels

Together, these tools provide a coherent framework for exploring metabolic interactions within food microbiomes and for identifying functional signatures associated with fermentation processes.

The article¹, authored by Julien Tap, Nacer Mohellibi, Colin Tinsley, Valentin Loux, and Stéphane Chaillou, describes the conceptual framework, design, and open-access resources of F3M.

Access the resources:

Learn and practice with the F3M R tutorial

A complete tutorial and training guide is available online for users who wish to become familiar with the F3M workflow:
https://fme_team.pages-forge.inrae.fr/f3mr/getting-started.html

This hands-on guide introduces the main steps of analysis with the f3mr R package, including:

Build a reference database from functional and taxonomic annotations.
Import sample count data .
Aggregate counts by taxonomic and functional levels.
Build a count matrix for downstream statistical analyses.

Each section of the tutorial includes example code and data to help users reproduce a full workflow, from raw annotations to interpretable metatranscriptomic profiles.

Tap et al. Food Microbiome Metabolic Modules (F3M), a tool suite for functional profiling of food microbiomes. Open Research Europe. 2025 ↩

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 ↩

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 ↩