Integrated Microbiome Research

Microbiomes surround us in both natural and man-made environments, playing a crucial role in human and animal health, food production, agriculture, and environmental bioprocesses. The understanding and application of microbiomes requires quantification of redox reactions in relation to the molecular properties of the system. During the doctoral course Integrated Microbiome Research participants will be introduced into the methodologies developed in the UNLOCK research infrastructure to identify the quantitative physiology of a microbiome in relation to its molecular properties. To achieve this, all participants will conduct a bioreactor experiment, process the data, make a process model, and conduct molecular analysis of the microbial community established. 

Target group

The course is aimed at professionals in Microbiology, Microbial Ecology, or Environmental Engineering, who wish to enhance their skillset for identification of dynamic cause-effect relationships in microbiomes. Researchers from different backgrounds like food microbiology or microbe-host interaction are welcome to attend. Depending on the background some aspects of the course may be more or less demanding for the different participants, but we aim to tailor the assistance towards the participants’ needs.

Learning Objectives

• Defining and conducting a bioreactor experiment for determining the quantitative physiology of a microbiome
• Processing of data acquired in a short-term bioreactor experiment
• Analysis of the metagenome development during the experiment
• Modelling of the fluxes established in the microbiome as a function of the activity of the different guilds of microorganisms involved
• Comparative analysis of the experiments conducted by the different course participants

Course Design

It is a hands-on course based on bioreactor experiment conducted by the participants. Emphasis is on processing and interpretation of the experimental data generated combined with computational modelling of the quantitative physiology of the microbiomes investigated. The experiments are accompanied by introductory lectures and exercises and computational work on the data gathered in the experiments.

During the course there will be ample time for discussion with teachers on your own research project, the benefits and pitfalls of the individual methods.

The course consists of 3 days in Delft (13-15 October) for conducting a bioreactor experiment at the Parallel Cultivation Platform of UNLOCK at TU Delft and processing of the data generated. The next 4.5 days (16-22 October) in Wageningen with emphasis on metagenomic characterization of biomass samples obtained during the Delft experiment, and processing, modeling and interpretation of all data. 

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