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

"FAIRification of multiOmics data to link databases and create knowledge graphs for fermented foods" MSCA-DN-JD Doctoral Network.

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.     

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.

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.

Objectives:

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.

Location and planned secondments:

The secondment schedule will be as follows:

• The first and third secondments will occur at NIZO Food Research, NL, with Marjon Wells-Bennik at months 15 and 27 for a duration of 4 months each 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 at month 20 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:

1st-degree awarding organisation: University of Reading, Reading UK https://www.reading.ac.uk/ 
2nd-degree awarding organisation: Wageningen University, Wageningen, Netherlands, https://www.wur.nl/en/wageningen-university.htm

Supervisors team:

The team of supervisors comprises of:

• Dr. Kimon Andreas Karatzas (M; main supervisor; Department of Food and Nutritional Sciences, University of Reading, UK) is a Faculty member (Associate Professor in Food Microbiology) at the Department of Food & Nutritional Sciences, University of Reading. His scientific outputs include more than 55 articles in high-impact journals (h-index of 26 based on SCOPUS), two international patents and various chapters in books. In the past, he successfully supervised 10 PhD students as main PI and 12 as Co-I, and nine postdoctoral researchers and visiting scientists. He has long experience in microbial physiology of stress and molecular biology and over 22 years of experience in food fermentations.
• Dr Marjon Wells-Bennik (F; secondary supervisor, during the secondment at NIZO BV) is a Principal Scientist at NIZO with extensive expertise in food microbiology, including fermentation and safety of plant-based dairy alternatives. She initiated various consortium projects with multiple academic and industrial stakeholders, including a recent project on “Microbial contaminants in plant-based protein ingredients”. Since 2002, she has supervised 8 PhD students; 2 are ongoing, and 6 obtained their degrees. She has published over 70 research articles and filed two patents. She can transfer fundamental knowledge to more applied research.
• Dr. Marilena Dasenaki (F) is an Assistant Professor at the Laboratory of Food Chemistry of the National and Kapodistrian University of Athens. Her research activity focuses on the study of food metabolomics using cutting-edge mass spectrometric techniques and advanced chemometric tools. Overall, Dr Dasenaki’s research has been published in 39 peer-reviewed papers and three book chapters, attracting more than >950 citations, with an h-index of 15, and her work has been presented at several international scientific conferences.
• Dr. Vasilis Valdramidis (M; secondary supervisor during the secondment at the National and Kapodistrian University of Athens) is an Associate Prof at the National and Kapodistrian University of Athens (Department of Chemistry). He holds a Ph.D. degree in Chemical Engineering from the Catholic University of Leuven, Belgium and a primary degree in Agriculture (Food Science and Technology) from the Aristotle University of Thessaloniki (Greece). He has about 100 publications in peer-reviewed Journals and chapters. He supervises/-ed eight post-doctoral researchers and more than 10 Ph.D.s (as main or co-supervisor) and acted as external examiner of several PhD Thesis across Europe.

Host institutions description:

The University of Reading is a public non-profit body. It is one of the leading universities worldwide and the top university in the UK in the area of Food Sciences (www.reading.ac.uk/food). It currently has more than 13,000 students, of which 1/3 are postgraduates and 2/3 are undergraduates.

NIZO Food Research is an advanced, independent contract research company. It is a small/medium-sized company (SME) with over 70 years of experience in dairy and non-dairy science and technology. NIZO has an annual turnover of around 13 M€. Its 100 employees (80 fte) successfully assist large multinational food and ingredient companies and start-ups to make better foods and be more profitable. NIZO applies expertise and competitive technologies to support innovation and cost reduction for customers.

The National and Kapodistrian University of Athens (NKUA), officially founded on April 14th, 1837, is the first University not only of Greece but both the Balkan peninsula and the Eastern Mediterranean region. The main sources of funding of NKUA are European, international and national funds, like for example, the Partnership Agreement (PA) for the Development Framework, 2014-2020 (European Structural and Investment FundESIF), Horizon 2020, as well as partnerships with public and private sector bodies, the provision of services to legal entities and individuals, grants and donations. The Dept of Chemistry (DoC) will be involved in the project. DoC has expertise, state-of-the-art infrastructure and facilities available for performing research in the areas of food science, food chemistry, environmental chemistry and water diagnostics. It also has expertise in the coordination and implementation of research and development activities, dissemination, and exploitation activities with national mainly stakeholders, e.g., the Hellenic Food Authority, and private food companies that export all around the world.