In 2026 and 2027, the #DominoEU project will continue to explore new aspects of the beneficial relationship between fermented foods and health. Special thanks go to the project’s PhD students, who led an interactive session with the project’s senior researchers, engaging in an open discussion on the future prospects of multidisciplinary projects like DOMINO, as well as the impact of AI on data management and computational tools.

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https://www.domino-euproject.eu/

This workshop was organised in the framework of the Domino project, with a strong focus on enabling partners to manipulate the F3M tool suite for microbiome data integration, gene catalog construction, and functional interpretation.

The morning sessions introduced the conceptual foundations of the F3M curated database and the associated tools.

Participants were then guided through practical use of the f3mr R package, focusing on data aggregation at both taxonomic and functional levels, normalization, and differential analysis workflows (notably using DESeq2), followed by integration into phyloseq for downstream functional mining.

See the tutorial here

After a working lunch, the afternoon sessions shifted toward more advanced tasks. Participants explored how to map metagenomic reads onto an existing F3M-inferred gene catalog, and how to construct a custom gene catalog from a defined list of microbial species. The tutorial, developed by Mohellibi Nacer, Stéphane Chaillou, and Valentin Loux, provided a complete pipeline:

• Mapping reads to a reference gene catalog using f3m_builder map
• Building gene catalogs from pangenomic inputs using f3m_builder build_catalog
• Exploring outputs in R using f3mr

The training relied on the Migale HPC infrastructure, with both interactive (qlogin) and batch (qsub) execution modes, ensuring scalability and reproducibility of analyses.

A key outcome of the workshop is that participants are now able to move across the full workflow: from raw sequencing reads to structured functional profiles linked to metabolic modules. This enables a tighter integration between microbial composition and functional potential in food microbiome datasets. The session ended with discussions on applications, including the design of microbial consortia and the exploitation of F3M modules for hypothesis-driven microbiome engineering.

Thank to CSIC for hosting.

The session, chaired by Damien Paineau, Ferments du Future CEO, brought together researchers and industry leaders working on biotechnology and sustainable food systems. Discussions spanned microbial fermentation, cellular agriculture, and scalable production systems, highlighting convergence across disciplines.

The BIOKET session emphasized a shared constraint across technologies: scaling from lab to industry. As highlighted by sessions speakers, success depends on robust bioprocess design, scalable production systems, and strong public–private partnerships. Within this landscape, SynthPlex contributes a complementary approach: engineering microbial ecosystems rather than single strains or cell lines. The long-term objective is clear: design fermented foods that are both functional and microbiome-aware, using rationally assembled microbial communities adapted to plant substrates.

cFMD is an incredible Food microbiomes metagenomic database for food microbiologists allowing the mining of microbiome taxonomic and functional information across more than 3,000 food samples.

This review focuses on community-level genome or metagenome-scale metabolic modeling as a strategy to rationalize and predict microbial interactions in food. We underline its power as a cornerstone in comprehensive and rational strategies for optimization of microbial consortia assembly, whether they are used in bottom-up or top-down approaches.

A specific thanks to Elham Karimi, postdoc in the FME lab, who brought this discipline into the scope of our research group and which we now apply in many of our projects, including in the ANR metasimfood project and the European #DominoEU project.

Stéphane Chaillou opened the session with an overview of the complex relationships linking fermented foods, gut microbiome modulation, and human health, presenting recent evidence on the variability of individual responses and the need for integrated approaches combining top-down and bottom-up strategies. His talk highlighted how microbial diversity in fermented foods and differences in clinical designs contribute to heterogeneous outcomes, and how innovative frameworks—including microfluidics, organoid systems, and metabolic modelling—can guide fermented-food microbiome engineering for health

Julien Tap then presented new results from the French Gut cohort, illustrating how large-scale shotgun metagenomics combined with extensive dietary and lifestyle metadata reveal ecological branches of the gut microbiome across the French population. These branches capture gradients of diversity, diet quality, and lifestyle, and can be predicted using questionnaire data. Julien also showed how dietary patterns themselves form branch-like structures associated with gut diversity, and how food exposome signatures (e.g., residual DNA) complement questionnaires to refine diet–microbiome analyses

A central message emerges clearly: people do not respond to fermented foods in the same way. Individual variability is striking, and the gut microbiome may plays a key role in shaping these differences. The authors emphasize that baseline microbiome composition and function may influence how individuals metabolize and benefit from fermented foods. Despite this growing evidence, mechanistic studies remain scarce, and the field still lacks precision-nutrition frameworks needed to predict who will benefit most.

The review also identifies major gaps: limited standardization of study designs, inconsistent reporting, and insufficient stratification between responders and non-responders. Addressing these limitations will be essential to move from broad dietary recommendations toward targeted, personalized strategies involving fermented foods.

As interest in microbiome-driven nutrition continues to rise, this work provides timely guidance for researchers and practitioners aiming to connect fermented food consumption with measurable, individualized health outcomes.

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.

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:

• F3M database
• F3M builder
• f3mr R package

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:

1. Build a reference database from functional and taxonomic annotations.
2. Import sample count data .
3. Aggregate counts by taxonomic and functional levels.
4. 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.

On 2 July 2025, the closing meeting of the EMOVOL (Molecular Ecology of Processed Poultry Meat) project was held at the Fleury Michon site in Pouzauges.

This project, which began in 2020, ran for five years (one year of set-up and four years of implementation). It followed on from an initial collaboration between the FME (Microbial Ecology of Food) team at the MICALIS institute, INRAE Jouy en Josas and Fleury Michon, which began in 2017 as part of Marine Zagdoun’s CIFRE thesis. Marine was hired by Fleury Michon after completing her thesis to carry out this new project.

A scientific approach serving industrial innovation

The aim of this ambitious project was to develop a method for assessing the preservation potential of batches of cooked processed poultry meat by quantifying certain microbial biomarkers present in the raw meat used to produce these same batches.

It was carried out in four stages:

Success driven by complementary expertise in research and industry

The expertise of the FME team, combined with Fleury Michon’s industrial know-how, was a major asset in developing a prototype conservation management tool designed to monitor and optimise processing routes to ensure proper product preservation. In this context, INRAE researchers contributed their knowledge of food microbiomes and their expertise in large-scale data processing, while Fleury Michon provided precise and essential knowledge of the entire production process, as well as expertise in microbiology and modelling.

An innovative solution deployed within the company

Committed to meeting consumer expectations in terms of naturalness and environmental friendliness, Fleury Michon strives to reduce salt, preservatives and packaging in its products. Although these changes are virtuous, they can impact sensory quality over time: taste, texture and, in particular, shelf life. This therefore requires precise monitoring of the microbiological quality of products.

To meet this challenge, Fleury Michon is rolling out an innovative solution, the result of a collaborative effort with INRAE: a method for characterizing the shelf life of cooked poultry charcuterie based on microbial biomarkers in raw meat. This method makes it possible to accurately monitor the quality of raw materials, guide manufacturing choices and guarantee the proper preservation of products.

This partnership has thus led to a scientific innovation applied to industry that is in line with INRAE’s mission to support its partners in co-developing concrete solutions for healthier and more sustainable food.

A special thanks

Food Microbial Ecology team (Stéphane Chaillou, Julien Tap, Marie Champomier-Vergès), Cosynus team (Young-Kyoung Park, Tritan Rossignol) from Micalis, Ferments du Futur (Damien Paineau), ICL Bioengineering department (Rodriguo Ledesma-Amaro, José Jimenz), ICL synthetic Biology department (Geoff Baldwin), ICL nutrition department (Gary Frost) and Bezos centre for sustainable proteins (Yvonne McMeel).