FAIROmics - PhD fellowship in Improving Predictive Power: Addressing Identifiability Challenges in Microbial Community Models.

"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 Vigo (UVIGO), Spain and the University of Leuven (KUL), Netherlands.

Objectives:

We are looking for 1 Doctoral Candidate (DC) to join our project at two sites in the EU (Spain and Belgium) with a master’s degree in a relevant discipline (Applied mathematics, Systems Biology, Bioengineering, or similar) interested in the dynamic modelling of microbial communities.

We seek a highly motivated and skilled Doctoral Candidate (DC) to join the Bioprocess and Biosystems Engineering  (Bio2Eng) group at IIM-CSIC (months 1 to 18), whereafter the PhD research will be continued at the Chemical & Biochemical Process Technology & Control (BioTeC+) group at KU Leuven/Campus Gent (months 19-36). The major aim is to develop theoretical methods and software tools to address the challenges of modelling microbial communities. The candidate will work on exploring and developing (1) identifiability analysis methods specifically devoted to ecological models and (2) novel model-based optimal experimental design (OED) methods with special emphasis on those accounting for biological variability. The candidate will combine ecological and coarse-grained models, identifiability, and OED concepts to define dynamic models that are able to characterise ecological interactions in microbial communities. Models obtained will be tested using data obtained in previous projects and within parallel studies within FAIROMICS. Methods developed will be released as open-source tools.

Expected results:

• Novel methods for the structural identifiability analysis of ecological models.
• Novel methods for model-based experimental design accounting for biological variability.
• Software tools to facilitate the application of developed theoretical and numerical methods.

Location and planned secondments:

The Doctorate Candidate will spend 18 months at IIM-CSIC in Vigo (Spain), whereafter the research will be continued for another 18 months at the BioTeC+ group of KU Leuven/Campus Gent (Belgium). KU Leuven/BioTeC+ is a multidisciplinary team at the interface of in silico systems biology and in vitro experimental predictive microbiology. Collaboration with the wet lab research is envisaged via experimental data exchange.

Enrolment in Doctoral degree:

1st-degree awarding organisation: University of Vigo, https://www.uvigo.gal/en
2nd-degree awarding organisation: KU Leuven, https://www.kuleuven.be/english/kuleuven/index.html

Supervisors team

The Biosystems and Bioprocess Engineering Group at IIM-CSIC (bio2eng.csic.es) focuses on understanding and designing biological systems and bioprocesses at different scales. Our research has wide-ranging applications, including industrial biotechnology and food processing. The Applied Systems Biology team, led by Dr. Eva Balsa-Canto, is where the Doctorate Candidate will work. The team uses hybrid-mechanistic modelling to study biosystems like microbial communities or microbial metabolism and to design novel bioprocesses of interest in the food and biotechnological industry. The team has significant experience in developing theory and methods related to model identification: structural and practical identifiability, sensitivity analysis, parameter estimation, model-based optimal design, dynamic optimisation and inverse optimal control.  We not only develop theoretical concepts, but we also create practical solutions such as software tools to facilitate the application of our research results.
Our research institute is located in the vibrant coastal city of Vigo, situated in Galicia, on the northwest coast of Spain. Vigo is a place where land and sea meet, offering picturesque beaches, fresh seafood, and a lively maritime culture.

The vision of BioTeC+ (Chemical & Biochemical Process Technology & Control) (www.cit.kuleuven.be/biotec) (PI Prof. Jan F.M. Van Impe) is to consolidate and strengthen both its international research position and its societal impact by focusing on a carefully selected number of research areas and application domains in applied chemistry/chemical and biological process engineering. At present, these application domains can be characterised by the keywords industrial biotechnology, closing the waste/water cycle, and public health. These constitute the pillars (columns) (bio)chemical reactions & reactors, (biological) waste(-water) treatment systems, and predictive microbiology/microbial risk assessment within BioTeC’s research matrix. This broad range of application domains is supported by our long-standing systemic (systems and control) approach towards applied chemistry/chemical and biological process engineering. The research areas (i) systems theory, systems biology and analysis, process model identification (including optimal experimental design), (ii) process monitoring, and (iii) optimisation and model-based control characterise the transversal rows in the research matrix. These rows constitute the longstanding fundament of BioTeC’s research covering and underpinning all application domains (pillars).

KU Leuven/BioTeC+ runs a state-of-the-art L2 accredited laboratory for experimental predictive microbiology research, as well as high-end computing facilities. Our five postdocs and 14 PhD researchers are involved in numerous international research projects and networks, including six ongoing EU projects. As a most international and inclusive team, we look forward to welcome you to our campus in the vibrant city of Gent, Belgium!

Host institutions description

The Spanish National Research Council (CSIC) is the largest public research organisation in Spain and one of the most important in the European Research Area (ERA). It is the main player in the Spanish Science, Technology, and Innovation System and is currently made up of over 13,200 people. These individuals are distributed between the CSIC Corporate Organization, 121 research institutes, and three national centres located throughout Spain, as well as an institute in Rome. The CSIC conducts research in three core areas: Society, Life, and Material, which cover most academic disciplines. In March 2021, the CSIC was among the institutions awarded the 'HR Excellence in Research Award'. The DC will be enrolled in the “Mathematical Methods and Numerical Simulation in Engineering and Applied Sciences” Doctorate program offered by the University of Vigo.

KU Leuven boasts a rich tradition of education and research that dates back six centuries and received the European HR Excellence in Research Award based on its current policy and a comprehensive action plan. The university’s basic research orientation has always been and will remain fundamental research. At the same time, the university remains vigilantly open to contemporary cultural, economic and industrial realities, as well as to the community’s needs and expectations. In the Times Higher Education ranking, KU Leuven is ranked as the 12th European university, while in the Reuters Top 100 of the World’s most innovative institutions, KU Leuven is listed as the first European university for the fourth year in a row. KU Leuven strives for an inclusive, respectful and socially safe environment. We embrace diversity among individuals and groups as an asset. Open dialogue and differences in perspective are essential for an ambitious research and educational environment. In our commitment to equal opportunity, we recognise the consequences of historical inequalities. We do not accept any form of discrimination based on, but not limited to, gender identity and expression, sexual orientation, age, ethnic or national background, skin colour, religious and philosophical diversity, neurodivergence, employment disability, health, or socioeconomic status. The DC will be enrolled in the Arenberg Doctoral School via the Faculty of Engineering Technology.