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

About the Project

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.

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.

Application deadline: 15/05/2024 23:59 – Europe/Brussels.

Envisaged job starting date: October 2024.

Hosting organisation: French National Institute for Agriculture, Food, and Environment (INRAE).

Planned secondment: One at the Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany, for a 12-month period.

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:

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.

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.

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.

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.
• Language: Applicants must demonstrate fluent reading, writing and speaking abilities in English (B2).

Recruitment process:

1. Candidates apply for a position using the online application form (ACCESSIBLE HERE).
2. The Project Manager provides a first screen of the written applications to check the eligibility of the candidate.
3. The DC supervisors will select the best candidates based on CV, academic records, recommendation and motivation letters and adequate skill set.
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.

For more information about the offer, the project and the recruitment process, please visit our website.