FERMENTED FOOD relies on the correct successive performance of raw food material modifications by different microbial populations. The control of this microbial ecology process depends on the type of fermentation (spontaneous with natural microbiota vs. starter controlled) and on abiotic factors (e.g. fermentation temperature, ingredients and preservatives). Although many food fermentation processes are ancestral and for some of them, now well mastered on an industrial production scale, it is important to understand that many of these processes will undergo changes.

CLIMATE & SUSTAINABLE FOOD PRODUCTION. Fermented food and beverage producers are facing three important environmental and technological challenges that will influence in the near future, if not already, their handling of the fermentation process. First, the reduction (or removal) of traditional preservatives (sulphite, nitrite, salt) is increasing the risk of failed fermentation (flavour defects, biogenic amines production) and of food waste. Second, the changes associated to progressive mutations in more sustainable agricultural practices modify the natural microbiota of the raw food and directly affect spontaneous fermentations. Third, global climate warming is affecting the properties (nutrient profiles) of raw fruits and vegetables. One may note higher sugar content in grape leading to higher alcohol content of wine, as well as higher or modified carbohydrate content of vegetables. Sometimes, the changes are forcing food producers to seek for new varieties adapted to longer and more frequent periods of drought, with subsequent downstream fermentation process modifications

A NEED TO DESIGN NEW MICROBIAL SOLUTIONS. It is therefore important to anticipate and predict the heterogeneous evolutions of the microbial ecology mechanisms that will take place in the fermented food process described above, and to find solutions focusing on sustainable approaches. Strategically, it is probably crucial to emphasize on leveraging microorganisms and their diversity rather than of the process itself. Food ecosystems are of relatively low complexity. This is a benefit for the comprehensive understanding of microbial functions and interactions during food fermentations

SYNTHETIC ECOLOGY: A NEW KEY DISCIPLINE IN MICROBIAL ECOLOGY. The project will develop a knowledge-based strategy using a Synthetic Ecology approach combining high troughput meta-omics analysis with ecological networks modelling for understanding how new tailormade microbial consortia could be built to overcome changes in fermented food. Wine (beverage, liquid fermented product) and fermented vegetables (solid fermented product) will be used as key two food models (generic concept) at the heart of this challenge. As shown in the figure below, the design of microbial consortia is one of the key method used in microbial ecology. The scientific approaches for designing new microbial consortia are of two kinds.

THE EVOLUTIONARY APPROACH. (On the left panel,). In this type of strategy, natural or artificial microbial communities (synonymous: microbial consortia, microbiota) are submitted to evolutionary processes whose objectives are to select functional communities with reduced biodiversity but whose function meets a need for innovation. It is therefore a top-down process oriented by selection and which seeks a predefined result, a target innovation. However, achieving a result is not guaranteed and maintaining the viability of the “selected” community remains a challenge.

THE SYNTHETIC ECOLOGY APPROACH. (On the right panel). It is the opposite approach, rather in a bottom-up process. It starts with the generation of hypotheses on the possible metabolic interactions within a microbial community in order to build an experimental approach whose objective is to test this hypothesis. It is therefore a repetitive, iterative strategy, since the results are used to reformulate the hypotheses and experiments to refine the level of understanding of the interactions when compared to data obtained from “natural” ecosystems. Synthetic ecology is therefore a basic science approach that can be the key to achieve a better control and innovation process in the field of microbial solutions for fermented foods through the gain of fundamental knowledge on metabolic interactions taking between the microbial species and between the food components and the microbial species.

CHALLENGES FOR WINE & VEGETABLES. They will be different on the two different food models. For wine, starter cultures are already widely used worldwide. However, there is a need to find new microbial solutions to face the changes arising from climate changes (increase of alcohol content, changes in phenolic compounds) and changes arising from new agricultural practices (organic production) or from societal demand (reduction of sulphites). For fermented vegetables, the fermentation of cabbages (sauerkraut) is the most common product traditionally produced in France. The fermentation process is still performed spontaneously. The challenge will be to assess how changes in agricultural practices, cabbages varieties, fermentation recipes (e.g. size of chopping) and changes in conservatives (salt) might influences the microbial interactions. Furthermore, additional fermented vegetables such as turnip, radish, carrot and beet are becoming more popular and it is not known if the microbial solutions could be generic to all vegetables or specific to each of them. The figure 1 below describes how the synthetic ecology pipeline of our project is going to be set up on the two food models.

The main research objectives of the project are:

1. To develop a common integrative multi-omics methodology for the two food models avoiding methodological locks that characterize microbial ecology approaches on fermented foods.<:p>

2. To leverage the extensive strain biodiversity preserved in our consortia’s Biological Resources Centres (BRC) for the careful construction of a wide range of artificial communities (fungi, bacteria and viruses) based on the association of functional properties required to fit the expected ecological network.

3. To model the role of candidate biotic and abiotic parameters into the changes in metabolic interactions induced by the environmental modifications. In turn, it will strengthen our ability to measure the adaptability of each fermentation system, the resilience of several tailor-made microbiota toward increased variations in the process.

4. To produce hypotheses on the evolution of food ecological networks (prediction) and subsequently be able to propose microbial solutions to overcome (prevention) deleterious changes.

5. The final step of the METASIMFOOD project is to validate the efficiency of the solutions proposed by the synthetic ecology pipelines in real food and at pilot scale. Firstly, sensorial validation will help us to assess whether there are aspect of known fermentation processes that must be maintained as present in the industrial context or that could be adapted to take account of the changed context of the model. The production of our knowledge will confirm or invalidate the processes in place within the industry, to confront this knowledge to choices already made empirically in the corresponding sectors and will provide guidelines for moving to more sustainable production meeting the societal demand.

The general working organisation of METASIMFFOD project and how the strategy will be implemented in research tasks is described below:

WP1 CONSTRUCTION AND VALIDATION OF STERILE SIMPLIFIED FOOD MODELS. will focus on the construction of simplified and sterile food models as close as possible to real food. The food models will be constructed with the aim to preserve the metabolic profiles of the real food matrices.

WP2 CONSTRUCTION OF ARTIFICIAL MICROBIAL COMMUNITIES. The principal objective will be to associate representative isolates of microbial actors including yeasts, bacteria and viruses, starting from a large pool of strains carefully selected based on their genomic content and possessing different ecological roles and functional traits. For each food model several type of communities will be designed to map a wide range of taxonomic and functional diversity.

WP3 MODEL DESIGN FOR THE SYNTHETIC ECOLOGY APPROACH. The main objective will be to construct appropriate mathematical models for each type of food enabling the proper evaluation and prediction of the impact of variables linked with future changes on the fermentation processes. It is highly interwoven with three experimental subtasks planed in Task 4.

WP4 EXPERIMENTAL TASK FOR THE SYNTHETIC ECOLOGY APPROACH. GENERATION OF OMICS DATA. The objective is to execute the plans produced in task 3 and generate the data to feed the models and build the ecological networks. It also includes the final validation, in real food and at pilot scale, of the solutions proposed from the SE approach developed in the project.

WP5 OPEN DATA MANAGEMENT. The project will generate a large amount of heterogeneous data. We will follow the recommendations of the ANR to pursue an Open Science strategy throughout the project. We will rely on the tools and support set up by INRAE with its Open Science charter and associated software.

WP6 PROJECT MANAGEMENT & DISSEMINATION OF RESULTS. This task will provide information workflow between partners and synchronization in tasks’ execution for the achievement of the project during the four years of its duration.

Providing non-specialist audience with essential scientific information on fermented foods. Our strategy of strong communication towards the general public (Conferences for the general public, events (museum); direct exchanges with the actors of participative sciences or regional associations), using dedicated content, appropriate vocabulary and interfaces adapted to any public, will serve as strong impact to explain the microbial ecology of fermented products with popularization aim.

A strong foreground to develop downstream innovative research programs with industrial stakeholder in fermented food area. The project will be a solid basis for developing innovative downstream research programs with industrial players in the field of fermented foods. Our project will deliver An Open Access database and computational tools to crystallize these future partnerships. The knowledge obtained on solid food models of plant origin (vegetables) could be used to develop similar approaches for the design of products from new plant sources / or intended to value agricultural and food waste in order to improve sustainability and circularity. Finally, our project will have a clear impact on the process of better exploiting microbial diversity for the production of many foods involved in human health.

A project that brings the synthetic ecology (basic science front) to the heart of food microbiology. The project will raise important fundamental questions about the role of microbial diversity in food safety and quality. It will demonstrate the benefit of this new multidisciplinary scientific strategy to other scientific questions related to fermented foods (e.g. impact on health benefits).