FAIROmics - PhD fellowship in Multi-omics data production during olive fermentation.

"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 National and Kapodistrian University of Athens (NKUA), Greece and the Wageningen University (WU), Netherlands.

Objectives:

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 Chemistry, Analytical Chemistry, Biotechnology, Food Microbiology) interested in multi-omics data production and comprehensive compositional understanding during olive fermentation.

The main objectives of this research project are to study microbial communities and to design plant-based food production, to explore fermented foods and to produce multi-omics data during olive fermentation. Metagenomics and transcriptomics coupled with metabolomic approaches will be used to comprehensively characterise the impact of microbiome on the chemical composition of table olives and other plant-based substrates and define the dynamic changes in key metabolites, determining their nutritional and sensory qualities during the fermentation process. Metagenomics, transcriptomics and metabolomics data will be produced according to the FAIR principles, using cutting-edge analytical methodologies and advanced chemometric techniques.

The analysis of the metabolomics, metagenomics and transcriptomics data will result in the identification of the microbial communities, microbes, metabolites and functional genes and their role in olive fermentation. Elucidating the metabolic pathways underlying the production of the quality- and flavour-determining components can lead to the optimisation of the fermentation process and to the effective monitoring of food quality changes.

Location and planned secondments:

The PhD student will mainly be located at NKUA in Athens, Greece for 27 months. Two secondments are planned :

• One in NIZO Research Company in Ede, Netherlands for 3 months to verify the growth, the acid production and the volatile production of L. plantarum strains on different plant-based substrates.
• One in the University of Reading, United Kingdom for 6 months to do shotgun sequencing and meta-transcriptomics.

Enrolment in Doctoral degree:

1st-degree awarding organisation: National and Kapodistrian University of Athens, https://en.uoa.gr/
2nd-degree awarding organisation: Wageningen University, https://www.wur.nl/en/wageningen-university.htm

Supervisors team:

The supervisor's team will be composed of Assistant Professor Marilena Dasenaki and Associate Professor Vasilis Valdramidis from NKUA, Associate Professor Kimon-Andreas Karatzas from UREAD, Dr Marjon Wells-Bennik from NIZO and Professor Marcel Zwietering from Wageningen University. All of them have ample experience in Food Chemistry and Food Microbiology and have supervised numerous PhD students.

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 45 peer-reviewed papers and four book chapters, attracting more than >1100 citations, with an h-index of 18, and her work has been presented at several international scientific conferences.

Dr. Vasilis Valdramidis (M) 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.

Dr. Kimon A. G. Karatzas (M) is a Faculty member (Associate Professor in Food Microbiology) of the Department of Food & Nutritional Sciences, University of Reading. His scientific outputs include more than 55 articles in high-impact journals (h-index of 23 based on SCOPUS), one international patent and various chapters in books. He is also a member of the ASM and SGM and the Editorial Board of Microbial Physiology and Metabolism, Frontiers in Microbiology and of the journal Foods. Currently, his group comprises 6 PhD students (2 will complete their studies in a few months) while he is co-supervisor of 3 more PhD students. In the past, he successfully supervised 9 PhD students as main PI and twelve as Co-I and nine postdoctoral researchers and visiting scientists. He has long experience in microbial physiology of stress and molecular biology and more than 22 years of experience in food fermentations. He conducted one of the first studies looking at the probiotic properties of isolates from fermentations of olives which is highly relevant to this project. He also has long experience in the fermentation of traditional products; he has conducted the first work of analysing the microbiota and using starter cultures for the production of lafun, a traditional casava-fermented Nigerian product. He also has a strong collaboration with various relevant companies and other scientists in the area.

Dr. Marjon Wells-Bennik (F) 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 degree. She has published over 70 research articles and filed two patents. She can transfer fundamental knowledge to more applied research. (FTE: 0.1)

Dr. M.H. Zwietering (M) is the Head of  WU-FHM which groups two personal professors, two associate professors and one assistant professor and approximately 30 scientists that aim to understand the behaviour of food-associated microbes to ensure the quality and safety of food. The research areas go from genomics and eco-physiology to risk assessment of food-associated microorganisms in food supply chains. Both aspects of food safety, food spoilage and fermentation are investigated.

Host institutions description:

In 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 coordinating and implementing research and development activities, dissemination, and exploitation activities with national mainly stakeholders, e.g., the Hellenic Food Authority, and private food companies that export worldwide. The key facilities of the Department of Chemistry of NKUA include cutting-edge, high-resolution mass spectrometric systems (LC-TIMS-TOF/MS, LC-QTOF/MS, GC-APCI-QTOF/MS) used for the HRMS analysis of the molecular ‘fingerprint’ of foodstuff following advanced target and non-target screening workflows. Additionally, there is full access to applied microbiological analysis for bacteria and fungal contaminants as well as techniques for mycotoxin identification.

Wageningen University is an internationally leading education and research organisation in life sciences with more than 10,000 students (of which 25% are from abroad). WU participates through the Laboratory of Food Microbiology, FHM (www.wur.nl/fhm). WU-FHM is headed by Prof. M.H. Zwietering and groups two personal professors, two associate professors and one assistant professor and approximately 30 scientists that aim to understand the behaviour of food-associated microbes to ensure the quality and safety of food. The research areas go from genomics and eco-physiology to risk assessment of food-associated microorganisms in food supply chains. Both aspects of food safety, food spoilage and fermentation are investigated. Wageningen University has fully equipped microbiological labs both for fermentation research and for food safety research (MLII).