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Closed for Applications



Early Stage Researcher (ESR5)  

PhD fellowship in Metabolomics and kinetic studies of microorganisms involved in cheese ripening

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 Eur 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 action of yeasts,  moulds and ripening bacteria, which can grow parallel orsequentially in the cheese curd, results in the production of flavour compounds. These flavour compounds are produced when there is an accumulation of metabolites due to a   slow-down of the central metabolism when substrates, cofactors,   oxygen or metals become unavailable.   Metals are involved in all biological processes,  as cofactors of many enzymes. Iron in cheese is linked to various components such as proteins, carbohydrate or citrate. Milk lactoferrin is a mammalian protein belonging to the transferrin family able to bind two ferric ions. The high stability constant of the iron-protein complex confers to lactoferrin anti-microbial activity leading to low iron availability for microorganisms in the curd. Species competition or mutualism depending on iron bioavailability can be one factor responsible for the structuring of the surface ripening microorganisms which are strict aerobe and need iron for their electron transport chain. Central carbon metabolism,   amino acid and fatty acid metabolisms linked to iron metabolism are key metabolic processes involved in the production of flavour in fermented products.    The effect of iron on the metabolism of ripening microorganisms,   alone or in consortia,   will be studied in controlled conditions. Growth parameters will be identified, a predictive growth model will be done to better anticipate complex ecosystem understanding. Metabolomics data will be collected and analysed. The results will be used to constrain a microbial community genome-scale metabolic model by   ESR1   (VUA).   One microorganism will be selected for further studies by the   ESR.   Physiological and transcriptomics data will be collected and a genome-scaled model will be developed thanks to planned secondments.

Expected Results

To identify the parameters that will allow the prediction of the evolution of the ripening process.

Planned Secondments

In total, 3 months will be spent at Actalia in France (growth parameters identification), 3 months at the Christian Hansen A/S in Denmark (transcriptome differential gene expression analysis in response to different iron concentration for one selected strain),  3 months at the Stichting VU in the Netherlands (constraint metabolic model).

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

  • chemistry and biochemistry skills

  • LC-MS and GC-MS experience (Appreciated)

  • 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 supervisor is S. Landaud-Liautaud who works as Professor at AgroParisTech, Communautés Microbiennes Alimentaires lab (CoMiAL) in Grignon, France. She is supervisor of 7 PhD, where 3 are hired in the private sector, 1 in an international institution, 1 in the academic sector and 2 students in progress, 19 Masters, 2 Post-Doc. The co-supervisors are S. Helinck – Associate Professor at AgroParisTech, Communautés Microbiennes Alimentaires lab (CoMiAL), Dr. D. Swennen (INRAE) - 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 S. Chuzeville (ACTALIA) – project leader in dairy microbiology, expertise in dairy starters, ripening bacteria, food spoilers and microbial ecosystems of dairy products.

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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