FAIROmics – PhD fellowship in plant-based food fermentation genomics.

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. However, they are not always reusable because they are difficult to find and access and because databases are not systematically interoperable.

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.

Hosting organisation : NIZO Food & Research BV, Ede, Netherlands.

Please note that this PhD position will lead to the award of a double diploma from Wageningen University and Research (NL) and the National and Kapodistrian University of Athens (NKUA). (Greece).

Applications Deadline 15/05/2024 23:59 – Europe/Brussels.

Envisaged job starting date: September 2024.

We are looking for a Doctoral Candidate (DC) to join our project at multiple sites in Europe with a master’s degree in Food Microbiology/Molecular Microbiology/Analytical Chemistry/Biotechnology/Biochemistry/Bioinformatics who is interested in new concepts to develop safe innovative plant-based fermented foods based on genome mining of starter bacteria.

The main objective of this research project is to rationally design mixed bacterial cultures to ferment plant protein-based ingredients with desirable outcomes. This will be based on predictions derived from available data sets on individual lactic acid bacteria (LAB) strains (with available sequenced genomes) and favourable fermentation outcomes upon growth on different plant-based substrates. Strain capabilities relevant to the preservation and safety of plant-based products will be determined. The performance of mixed cultures to ferment plant-protein-based ingredients regarding the formation of favourable flavour compounds, removal of unwanted chemical contaminants (e.g. off-flavours, mycotoxins), and acid formation and preservation effect (suppressing the growth of spoilers and pathogens) will be verified. Linking of functional properties of strains and genomic traits with fermentation outcomes will support the design of novel fermented foods.

The project is expected to generate a model to predict outcomes of different plant protein-based fermentations using mixed cultures of lactic acid bacteria with respect to flavour formation, removal of unwanted compounds, and preservation capacity. This allows for steering relevant fermentation outcomes based on key gene functions and fermentative capacity of LAB strains on different plant-based substrates.

Required skills/qualifications:

• Master’s degree in Food Microbiology / Molecular Microbiology / Analytical Chemistry / Biotechnology / Biochemistry / Bioinformatics with demonstrable affinity for microbiology and data science.
• Knowledge of and experience in working in a microbiological or biochemical laboratory.
• Affinity with complex data analysis and interpretation.
•  Affinity with genome-based data analyses is favoured.
• Excellent planning and analytical skills.
• Open collaborative communication style with attention to the team.
• Excellent writing and presentation skills.
• Proactive attitude with a strong sense of responsibility.

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.

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).

* EXCLUDED: short stays such as holidays, compulsory national services such as mandatory military service and procedures for obtaining refugee status under the General Convention.

Recruitment process:

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.

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