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Closed for Applications



Early Stage Researcher (ESR10)  

PhD Fellowship in Cheese microbial ecosystem structuration and resilience 

Project Title

“E-MUSE Complex microbial ecosystems multiscale modelling: mechanistic and data driven approaches integration” MSCA-ITN-2020 European Training Network

Hosting Organization


Researcher Profiles


Research Field

Food microbiology, molecular microbiology, cheese process, flavour formation, (bio)process modelling

Application Deadline

prolonged till 1st April 2021 00:00 - Europe/Brussels

Envisaged Job Starting Date



3 years

Contract Type

full-time employment (based on COVID-19 evolution and restrictions, possibility to start remotely, once situation allows the presence is required)


€3 783.39 gross salary/month

+ €600 gross mobility allowance/month and €500 gross family allowance/month (if applicable)

Taxation and Social (including Pension) Contribution deductions based on National and company regulations will apply.


The objective of the ESR10 project is to understand the effect of iron on the cheese ecosystem. Dynamic data will be collected during the ripening process of a model cheese produced with/without iron supplementation. Several macro-scale data will be collected: microorganisms’ growth, substrates degradation, pH, colour, rheology, moisture, organoleptic properties, and online measure of respiration. The deduced macroscopic properties will be used by the modelling researchers to identify relationships with micro-scale features from multi-omics data collected in parallel (e.g. transcriptome, metabolome). The ESR will focus his/her studies on biochemical pathways involved in iron homeostasis, oxidative stress, sulphur metabolism and volatile sulphur compounds production to understand the effect of iron on the ecosystem’s equilibrium. These metabolisms are interconnected and largely contribute to important organoleptic properties of fermented foods through the release of odor-active compounds. The ESR will acquire integrative bioinformatics and statistics skills thanks to the planned secondments.

Expected Results

To understand the structuration and resilience of cheese microbial ecosystem. To identify the biomarkers that will allow the prediction of the evolution of the ripening process.

Planned Secondments

In total, 2 months will be spent at the Nizo Food Research BV in the Netherlands (high throughput cheese facilities), 3 months at the Institut Pasteur in France (bioinformatics and statistics),  1 month at the Universite Paul Sabatier Toulouse III in France (Integration with linear and non-linear methods) and 1 month at the Alma Mater Studiorum - Universita di Bologna in Italy (Network theory for integration)

Enrolment in Doctoral degree


Required Education Level

Master’s degree in in Microbiology, obtained no later than September 2021.

Skills / Qualifications

  • educational background and previous research experience relevant for the chosen position 

  • previous experience in omics data manipulation

  • bioinformatics skills, statistics (Appreciated)

  • networking and good communications skills (writing and presentation skills)

  • willingness to travel abroad for the purpose of research, training and dissemination.

Specific Requirements

For the eligibility please check: Eligibility Criteria

Required Languages

English: B2, good oral and written communication skills in English are compulsory

Supervisors Team

The presence of microorganisms in food products is due to the deliberate inoculation of microbial cultures, and also to growth of microorganisms present in the raw materials, processing surfaces, and the manufacturing environments. They form microbial communities whose composition and activity evolve during manufacturing and storage, and which impact the organoleptic and sanitary quality of the final products. The CoMiAL team aims to better understand the structure and functionality of these microbial communities. For this, it implements skills in the fields of genomic analyzes (bacteria and yeasts), genetic modification (yeasts), microbial ecology and physiology, and the characterization of microorganism / surface and microorganisms / microorganisms interactions.

The lead supervisors E. Dugat-Bony and P. Bonnarme are members of Paris-Saclay Food and Bioproduct Engineering research unit (SayFood) at INRAE, team Food Microbial Communities (CoMiAl). Eric Dugat-Bony does research in Food Microbiology, Microbial Ecology and Bioinformatics. He is also currently a supervisor of 1 PhD and 1 Master. Pascal Bonnarme (INRAE) is a Research Director at SayFood, team Food Microbial Communities (CoMiAl), specialized in microbial metabolism and fermented foods; The co-supervisors are Dr. D. Swennen (INRAE) – Researcher at SayFood, team Food Microbial Communities (CoMiAl), specialized in molecular biology and genetics of the yeast Yarrowia lipolytica. Dominique’s focus is to understand the structure and function of food microbial communities and their development over time using meta-omics and integrative approaches and A. Saint-Eve - Associate Professor at AgroParisTech, member of SayFood, team Interactions Man-Food for conception (IHAC), specialized in sensory analysis.

Host Institution Description

The French National Research Institute for Agriculture, Food, and Environment (INRAE) is a major player in research and innovation.
INRAE carries out applied research and resulted from the merger of INRA and IRSTEA on January 1, 2020. It is a community of 12,000 people with 268 research, experimental research, and support units located in 18 regional centres throughout France. Internationally, INRAE is among the top research organisations in the agricultural and food sciences as well as in the plant and animal sciences. It also ranks 11th globally in ecology and environmental science. It is the world's leading research organisation specialising in agriculture, food, and the environment.
INRAE’s main goal is to be a key player in the transitions necessary to address major global challenges. Faced with a growing world population, climate change, resource scarcity, and declining biodiversity, the institute is developing solutions that involve multiperformance agriculture, high-quality food, and the sustainable management of resources and ecosystems (

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