FAIROmics - PhD fellowship in Microbial ecology - Deciphering the role of bacterial-fungal interactions in plant-based fermented food.

"FAIRification of multiOmics data to link databases and create knowledge graphs for fermented foods" MSCA-DN-JD Doctoral Network.

The FAIROmics initiative, an interdisciplinary research programme, will gather universities, research centres and private companies to enable the FAIRification of omics data and databases interoperability and develop knowledge graphs for data-driven decision-making to rationally design microbial communities for imparting desirable characteristics to plant-based fermented foods in the context of open science and its regulations. The FAIROmics training programme aims to develop doctoral candidates’ skills at the interface between artificial intelligence, life sciences, humanities, and social sciences.     

Plant-based dairy and meat alternatives have grown in popularity in recent years for various reasons, including sustainability and health benefits, as well as lifestyle trends and dietary restrictions. However, plant-based food products can be nutritionally unbalanced, and their flavour profiles may limit their acceptance by consumers. Microorganisms have been used in making food products for millennia. However, the diversity of microbial communities driving plant-based fermentations, as well as their key genetic and phenotypic traits and potential synergies among community members, remain poorly characterised. Many data exist, but they are spread into different literature (scientific and grey) or, in the best case, in different databases. However, they are not always reusable because they are difficult to find and access and because databases are not systematically interoperable.

Please note that this PhD position will lead to the award of a double diploma after the completion of a stay in each of these organisations: French National Institute for Agriculture, Food, and Environment - INRAE (PhD title delivered by the Université Paris-Saclay) and Helmholtz Centre for Environmental Research - UFZ (PhD title delivered by the University of Leipzig).

Objectives:

We are looking for 1 Doctoral Candidate (DC) to join our project at multiple sites in the EU with a master’s degree in microbiology or microbial ecology interested in deciphering the role of bacterial-fungal interactions in plant-based fermented food using multi-omics data.

The objective of the proposed PhD project is to understand and predict the mechanisms involved in the fermentation process of plant-based foods. This project will explore both intra- and inter-domain interactions, using bacterial-fungal interactions in fermented food as model. Synthetic ecology will be used to design simplified communities able to ferment plant-based food and insure organoleptic quality of the product. A selection of microorganisms adapted to the plant-based matrix will done based on current knowledge and using multiple criteria. Using publicly available metabarcoding, genomics and metagenomics datasets of plant-based fermented food, taxa of interest will be selected for further exploration of their metabolic potentials in relation to the composition of the matrix. Therefore, synthetic communities will be defined for their functional potentialities (e.g. proteolytic, lipolytic, flavouring, debittering, texturing, appetising). Microcosm-scale experiments will be set up to monitor over time the fermentation process as well as to collect physicochemical (substrate degradation, pH, moisture, oxygen) and multi-omics (transcriptomics, metabolomics) data combined with stable isotope probing (SIP) to decipher the mechanisms of these interactions. By adding or excluding members of these communities, the importance of the bacterial-fungal interactions will be highlighted, with a focus on the identification of potential cross-feedings and synergy in the process of carbohydrate, fatty acid and protein degradation during the food matrix fermentation as well as a focus on the role of fungal highways. For instance, at the microscale, the formation of a niche for fermentation on the fungal hyphae can be explored.

All the datasets will be generated according to FAIR principles and thus, available to create knowledge graphs within the FAIROmics framework. This PhD project aims to develop stable and efficient communities for plant-based fermented food production but also to better understand the synergy between bacteria and fungi during plant-based fermentation processes.

Location and planned secondment:

The PhD student will be located at INRAE in Palaiseau, France, for 24 months. The secondment will be done at the Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany, under the supervision of Dr. Lukas Y. Wick for a 12-month period.

Enrolment in doctoral degree:

1st-degree awarding organisation: University of Paris-Saclay (UPSaclay), https://www.universite-paris-saclay.fr/en
2nd-degree awarding organisation: University of Leipzig, Germany, https://www.uni-leipzig.de/en

Supervisors team:

Dr. Vincent Hervé (M) is a researcher at the French National Institute for Agriculture, Food, and Environment (INRAE). He is a microbial ecologist working on microbial diversity (taxonomic and functional), microbial interactions and the contribution of microorganisms to ecosystem functioning. Recently his work has focused on fermented food.

Dr. Eric Dugat-Bony (M) is a researcher at the French National Institute for Agriculture, Food, and Environment (INRAE). He is a microbial ecologist working on the effect of biotic (e.g. bacteriophages) and abiotic (e.g. NaCl content) factors on the microbial ecosystems involved in food fermentation. His favourite model ecosystem is the cheese surface.

Dr. Pascal Bonnarme (M)  is a Research Director at SayFood, team Food Microbial Communities (CoMiAl), specialising in microbial metabolism and fermented foods.

Dr. Lukas Y. Wick (M) leads the ‘Bioavailability’ group at the Dept. of Applied Microbial Ecology at the Helmholtz Centre for Environmental Research UFZ in Leipzig, Germany. His interest relates to the bio-physical and ecological drivers of microbial activity in natural and built environments, and he is an expert on bacterial-fungal interactions and mycosphere processes.

Host institutions description

The French National Institute for Agriculture, Food, and Environment (INRAE) is a public research establishment bringing together a working community of 12,000 people, with 268 research, service and experimental units, located in 18 centres throughout France. INRAE is one of the world leaders in agricultural and food sciences, plant and animal sciences. Its research aims to develop solutions for multi-performance agriculture, high-quality food and sustainable management of resources and ecosystems. The SayFood UMR (Paris-Saclay Food and Bioproduct Engineering Research Unit) aims to contribute to product-process innovation that takes into account the constraints of upstream production, consumer needs and expectations, and environmental issues.

The Helmholtz Centre for Environmental Research - UFZ, Germany, is a centre in the Helmholtz Association of National Research Centres with ca. 1100 people. It is one of the world’s leading research centres in the field of environmental research, enjoying high social recognition. It demonstrates ways in which sustainable use of our natural resource base is possible for the benefit of both humankind and the environment. The Department of Applied Microbial Ecology Microbiology investigates complex microbial communities and their importance for the reliability of microbial ecosystem services. This knowledge finds its application in the development of ecologically inspired biotechnological approaches.