Job description
Title: DC1, PhD fellowship in Microbial ecology – Deciphering the role of bacterial-fungal interactions
in plant-based fermented food.
Researcher profile: Doctoral candidate.
Research field: Microbial ecology.
Type of contract: Temporary.
Job status: Full-time.
Duration: 36 months.
Application deadline: 15/05/2024 23:59 – Europe/Brussels.
Envisaged job starting date: October 2024.
How to apply: submit your application form through this link: https://sondages.inrae.fr/index.php/342264?lang=en
Hiring organisation and offer posting contact details
Organisation: French National Institute for Agriculture, Food, and Environment (INRAE).
Number of positions available: 1.
Country: France.
Address: : UMR SayFood, 22 place de l’agronomie, 91120 Palaiseau, France.
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).
Offer description
In brief:
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.
FAIROmics project:
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.
Scientific context:
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.
Objectives:
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.
Expected results:
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
Required skills/qualifications
Master’s degree in microbiology or microbial ecology or related field.
Knowledge in microbial ecology, microbial interactions, community ecology.
Knowledge in bacterial and/or fungal metabolism and physiology.
Experience in (meta)genomic and/or metabolomic data analysis.
Computational skills: R (preferred) or any other language suitable for data analysis.
Curiosity, Creativity and Autonomy.
Critical and independent mind.
Self-driven personality able to work both independently and in a team.
Prepared to work in an interdisciplinary environment.
Eligibility criteria
Any nationality
Doctoral Candidate (DC): The applicant must not have been awarded a doctoral degree.
Mobility rule: The DC must not have resided or carried out main activity (work, studies, etc.) in
the country of their host organisation for more than 12 months* in the three years immediately
prior to the date of selection in the same appointing international organisation.
* EXCLUDED: short stays such as holidays, compulsory national services such as mandatory
military service and procedures for obtaining refugee status under the General Convention.
Language: Applicants must demonstrate fluent reading, writing and speaking abilities in English
(B2).
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.
We offer
A comprehensive, interactive and international training programme covering the broader
aspects and interface between life science, data science, artificial intelligence and humanities and
social sciences, as well as transferable skills.
An enthusiastic team of professionals to co-operate with.
Personal Career Development Plan (PDCP) to prepare young researchers for their future careers
Each DC will undergo individual training at individual institutes according to the PCDP
description.
An attractive compensation package in accordance with the MSCA-DN programme regulations
for doctoral candidates. The exact salary will be confirmed and will be based on a living allowance
of 3400€/month (correction factor to be applied per country) + mobility allowance of
600€/month. Additionally, researchers may also qualify for a family allowance* of 660€/month,
depending on the family situation. Taxation and social (including pension) contribution
deductions based on national and company regulations will apply.
*family = be married/be in a relationship with equivalent status to a marriage recognised by the
legislation of the country or region where it was formalised/have dependent children who are being
maintained by the researcher.
Selection process
The selection process is based on the merits of providing equal opportunity and will be in agreement
with the European Code of Conduct for the Recruitment of Researchers.
1. Candidates apply for a position using the online application form (accessible here).
2. The FAIROmics Project Manager provides a first screen of the written applications to check
the eligibility of the candidate and forwards the eligible applications to the DC supervisors.
3. The DC supervisors will select the best candidates based on CV, academic records,
recommendation and motivation letters and adequate skill set. To better assess the best
candidate, the shortlisted candidates might be asked to write an abstract of provided scientific
documents relevant to the research subject.
4. The selected applicants will be interviewed through an online meeting by the Selection
Committee (two main supervisors and two representatives of a beneficiary or associated
partner, with at least one person external to the DC’s project).
5. The best candidates will be chosen by the main supervisors. The European Project Manager
will communicate the successful candidates to the Consortium and Partners.
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