FAIROmics – PhD fellowship in Food Microbiology – Omics-driven investigation of unique features of olive fermentation isolates beneficial for plant fermentation with probiotic properties.

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.

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

Envisaged job starting date: October 2024.

Hosting organisation: University of Reading, United Kingdom (UREAD).

Planned secondments: Two at NIZO Research Company in Ede, Netherlands of a duration of 4 months each and one at the National and Kapodistrian University of Athens (NKUA), Greece for a duration of 4 months.

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: the University of Reading (UREAD), UK and the Wageningen University (WU), Netherlands.

Offer description:

We are looking for one (1) Doctoral Candidate (DC) to join our project at multiple sites in the EU with a master’s degree in a relevant discipline (Food Microbiology, Biotechnology, Biology etc.) interested in the Phenotypic analysis of table olives fermentation and identification of important genetic mechanisms for fermentation of plant products and health.

Classical Microbiology techniques (acid resistance, growth properties, antimicrobial activity against spoilage organisms etc.) will be used to assess the general characteristics of representative olive fermentation isolates in terms of their usage as starter cultures in food fermentations, not only for olives but also for other plant-based foods. Additionally, the strains will be assessed for their potential probiotic properties (bile acid resistance, attachment to Caco-2 cells, antimicrobial activity against pathogens etc.). Subsequently, based on all data available, the role of target genes of L. plantarum will be investigated either by deletion or by expression in a heterologous host to study the role of these genes on the phenotype.

Expected results:

• Physiological, fermentative and probiotic characterisation of representative isolates of Lactiplantibacillus plantarum from olive fermentations, assessment of their anti-microbial activity against spoilage organisms.
• Functional genomics characterisation, identification of the role of GAD system.
• Validation of the ability of these strains to ferment at low salt environments and potential usage as starters in other plant-based foods.

Required skills/qualifications:

• Applicants should holda Master’s Degree or equivalent in subjects such as Food Science, Microbiology, Biomedical Sciences, Genetics, Biochemistry or relevant disciplines.
• Knowledge of basic Microbiology techniques.
• Knowledge of basic aseptic techniques.
• Knowledge of Molecular techniques is desirable but not necessary.

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.