SynComs are assemblies of microscopic organisms cultivated in the laboratory to study interactions between microbes and hosts (plants, animals or humans) or to develop concrete solutions such as microbial fertilizers, fermenting agents, probiotics or biopesticides. The word “synthetic” can be confusing, as it is associated with synthetic biology and genetic manipulation, whereas most of these communities are composed of naturally occurring, unmodified strains.

By adopting a more neutral and precise terminology, scientists hope to:

• facilitate public understanding and strengthen confidence in products that use microbiomes;

• harmonise communication practices across different sectors (agriculture, health, food, environment);

• simplify regulatory procedures, particularly in Europe where the legislation for “consortia of microorganisms” (Regulation 2019/1009) already accepts defined assemblies.

Recent studies already show that well‑characterised communities can increase crop resilience to stresses (drought, pathogens) and improve human health; for example, consortia of intestinal bacteria are being tested as alternatives to traditional probiotics. Thus, moving from “synthetic” to “Defined Microbial Community” could accelerate the development of sustainable microbiological solutions while avoiding the prejudice attached to the word “synthetic.”

Source : Read the article in Nature Communications

Related project: DOMINO

Julien’s presentation, “Next-Gen Fermented Food: Harnessing Gut Microbiome Diversity and Functions,” focused on a major challenge for nutrition and microbiome research: people do not all have the same gut microbiome and may therefore respond differently to the same dietary intervention or fermented food.

Large population studies show that measured host and environmental factors explain less than 20% of the variation in gut microbial composition. Diet and lifestyle remain important, but they are only part of the picture. Stochastic processes and ecological rules also contribute to the assembly and evolution of each person’s microbial ecosystem.

Julien highlighted microbiome resilience as a particularly important concept. Throughout life, the gut microbiome can experience dietary changes, medication, illness, and other disturbances. Its capacity to resist these pressures or recover from them helps maintain its structure and functions. Understanding this resilience is therefore essential when seeking to modulate the microbiome through food.

The symposium was also an opportunity for Julien to present preliminary results from the MicroEngine project. These results contribute to understanding how microbial ecosystems and their functions can be harnessed to support microbiome engineering between fermented foods and the gut. This work complements the broader ambitions of DOMINO and the Ferments du Futur Grand Challenge to develop healthy, sustainable, and scientifically grounded fermented-food innovations.

The central message was that the development of next-generation fermented foods should move beyond a one-size-fits-all approach. Their design should consider:

• the diversity of gut microbiome states across individuals;
• the ecological processes that structure microbial communities;
• the functions carried by these communities, not only their composition;
• and the resilience that shapes individual responses over time.

This ecological and functional framework can help guide the development of more targeted, effective, and sustainable fermented foods. It also strengthens the connection between population-scale gut microbiome research and food microbial ecology, two complementary areas at the heart of the FME team’s research.

The symposium also included presentations on sake yeasts, microbiome-driven strategies for health and treatment response, and taste-cell organoids for studying umami. Together, these contributions illustrated the value of French-Japanese scientific cooperation for advancing fermentation and food bioscience.

Source: INRAE-Tokyo NODAI Joint Symposium announcement on LinkedIn

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.

Don’t hesitate to stay connected to the project by checking our website or subscribe to our newletters.

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.