FAIROmics – PhD fellowship in identifying and controlling of key regulatory mechanisms for differential responses and metabolic shifts in microorganism populations

“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 CSIC – Insititute for Integrative Systems Biology (I²SysBio), Spain and the University of Paris-Saclay (UPSaclay), France.

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 (Master’s degree in engineering, physics, systems biology, applied mathematics, biotechnology) interested in Modeling, analysis and control of biological systems in the context of microbial fermentations.

Objectives:

Elucidating key genes, enzymes and proteins responsible for differential metabolic and cellular responses using model-based analysis techniques:

• Identifying the key regulators and most suitable variables for control of the fermentation/ripening process.
• Conceptualisation and formulation of the control problems to be addressed in order to drive the microorganism population to a desired state in order to meet the a priori desired product-specific control and optimisation objectives (including the control of key metabolic shifts) in the presence of uncertainty and molecular noise.
• Developing methods and software tools for the control and optimisation of gene regulation and metabolism of microorganism populations during the fermentation/ripening process.

Expected results:

• List of the identified key regulators and variables for control of the microorganism population.
• Definition of the control problems to be addressed in order to drive the microorganism population to a desired state.
• Methods and tools for model-based feedback control of the microbial population under molecular noise.

Location and planned secondment:

The PhD student will mainly be located at the  CSIC – Insititute for Integrative Systems Biology (I²SysBio) site in Valencia for 20 months. A secondment at the UMRSayFood – INRAE/AgroParisTech is also planned for a duration of 16 months.

Enrolment in Doctoral degree:

1st-degree awarding organisation: Universitat Politècnica de València https://www.upv.es/index-en.html
2nd-degree awarding organisation: Université Paris-Saclay https://www.universite-paris-saclay.fr/en

Supervisors team

The supervisor team is composed of Irene Otero-Muras (I2SysBio), Cristian Trelea and Emmanuel Bernuau (AgroParisTech). The PhD candidate will benefit from the research experience in dynamic modelling and automatic control in CSIC-I2SysBio and APT. Both partners develop complementary tools for model analysis, parameter identification, and multi-objective dynamic optimisation and have extensive experience with theory and applications of automatic control to biological processes. Specifically, at CSIC-I2SysBio, the DC will benefit from the expertise in advanced mathematical analysis and control of biomolecular systems (including regulation, signalling and metabolism), whereas at APT, the DC will develop theoretical and computational tools for dynamic system control during fermentation/ripening processes.

Host institutions description

Institute for Integrative Systems Biology: The Spanish National Research Council (CSIC-Agencia Estatal Consejo Superior de Investigaciones Científicas) https://www.csic.es/en/csic is an autonomous, multi-disciplinary public research body affiliated to the Spanish Ministry of Science and Innovation. The CSIC has its own legal structure and is represented throughout the Spanish territory with a total of 105 centres/institutes. CSIC is the first Spanish organisation in the Framework Program of the European Union by number of projects and economic return. The I²SysBio https://www.uv.es/i2sysbio is a joint research institute involving Universitat de València (UV) and CSIC. I²SysBio Scientific Programs focus on research into the structure, function, dynamics, evolution, and manipulation of complex biological systems.

AgroParisTech is a school of engineering in the field of life sciences https://www.agroparistech.fr/en, part of the Paris-Saclay University. The DC will be hosted at the Paris-Saclay Food and Bioproduct Engineering Research Unit (SayFood). This lab’s research interests are physical, biochemical and microbiological processes that govern the food and non-food transformations of bioproducts. SayFood is a joint research unit between AgroParisTech and INRAE national research institute on agriculture, food and environment https://www.inrae.fr/en.