Postdoc Computational Microbiome Ecology for Fermentation Technologies

Organisation/Company

Technical University of Delft

Research Field

Biological sciences

Researcher Profile

Recognised Researcher (R2)

Country

Netherlands

Application Deadline

15 Feb 2025 - 23:00 (UTC)

Type of Contract

To be defined

Job Status

Full-time

Hours Per Week

To be defined

Is the job funded through the EU Research Framework Programme?

Not funded by a EU programme

Is the Job related to staff position within a Research Infrastructure?

No

Anaerobic fermentative microbiomes growing on organic carbon simultaneously employ multiple biochemical pathways to maximize free-energy conservation. Despite their significant relevance to health, environmental science, and biotechnology, predicting their stoichiometry, kinetics, and ecological behavior under varied and dynamic conditions remains a challenge. Key ecological questions that would enhance our understanding of microbiome assembly and dynamics are still unanswered. For instance: Can we consistently direct population dynamics, restore lost functionalities, or select specific interspecies interactions? To what extent does inoculum composition influence community structure and function?
In the laboratory, we will cultivate fermentative communities in parallel bioreactors, subjecting them to controlled variable selective pressures (https://m-unlock.com/parallel-cultivation-platform ). These bioreactors are equipped for high-throughput biochemical and molecular analyses, which will reduce uncertainty in experimental data and support the generation of theoretical hypotheses.

Simultaneously, this project will further develop a multiscale modelling platform (https://github.com/Computational-Platform-IbM ) able to simulate bioreactor dynamics, mass transfer limitations, and microbial interactions. This digital twin will enable us to test theoretical derivations of microbial growth parameters grounded in bioenergetics and cellular resource-allocation principles. We hypothesize that competition for energy is crucial for the survival of syntrophic populations, which are at the core of any fermentative microbiome.
Through this project, we aim to advance the integration of mathematical modelling in biotechnological laboratory experimentation. Biotechnological research has traditionally relied on empirical approaches, which are often slow and costly. Computational platforms like the one we will develop in this project will promote a more quantitative approach to ecology, facilitating rational bioprocess design and driving innovation in the field.
This project is part of a large interantional consortia that joins efforts to find best practices for manure treatment from a technological, economical and social scopes. With the developed and fully matured computational model, the simulation of the bioprocesses involved in cutting-edge technologies for the treatment of manure wastes will be approached, contributing to decision-making and design when selecting and optimising the technologies involved for different case studies.  

The selected candidate will work in the section of Environmental Biotechnology of the Biotechnology Department. They will be part of a team of researchers working with computational models and microbial cultivations, regularly participating in internal meetings and seminars. They will contribute to science disemination by writing scientific articles and presenting their work in national and international conferences and symposia. Aditionally, the selected candidate will have oportunities for mentoring PhD candidates, Master and Bachelor students.

Website

https://jobrxiv.org/job/technical-university-of-delft-27778-postdoc-computation…

Number of offers available

1

Company/Institute

Technical University of Delft

Country

Netherlands

Geofield

Website

https://www.tudelft.nl/tnw/over-faculteit/afdelingen/biotechnology

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