Mots-Clés
Food Microbiology
Molecular Microbiology
Biotechnology
Biochemistry
, Bioinformatics
Description
PhD fellowship in Food Microbiology - Omics-driven investigation of unique features of olive fermentation isolates beneficial for plant fermentation with probiotic properties.
We are looking for one 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 microorganisms involved in table olives fermentation and identification of important genetic mechanisms for fermentation of plant products and health.
FAIROmics project:
The FAIROmics initiative (https://www.dn-fairomics.eu/), 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.
Scientific context:
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.
Objectives:
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.
Location and planned secondments:
The work in the project will partly be executed at the premises of collaborating organisations.
The secondment schedule will be as follows:
• The first secondment will occur at NIZO Food Research, NL, with Marjon Wells-Bennik for a duration of 6 months to work on Functional genomics to identify molecular mechanisms related to plant fermentation & probiotic properties (construction of mutants and cloning of important genes in L. plantarum).
• The second secondment will take place at the National and Kapodistrian University of Athens, Greece with Marilena Dasenaki & Vasilis Valdramidis for a duration of 4 months to work on verification of growth/acid production/volatile production of L. plantarum genetically modified strains.
Enrolment in Doctoral degree:
University of Reading, Reading UK https://www.reading.ac.uk/
Required skills/qualifications:
• Applicants should hold a Master’s degree or equivalent on 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.
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 (EXCLUDED: short stays such as holidays, compulsory national services such as mandatory military service and procedures for obtaining refugee status under the General Convention) 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).
You will find all the information about the offer on the website https://www.dn-fairomics.eu/open-phd-positions