Studying ecology and physiology of previously uncultivable anaerobic microbial communities.

Background

Metagenomics has revealed the existence of new strains and branches in the tree of life. These branches include microorganisms that have been uncultivable in the lab. However, with novel enrichment techniques and knowledge gained from metagenomic studies, new possibilities have unfolded towards enrichment and cultivation. With these new techniques, this project aims to study ecology and physiology of anaerobic microbial communities focussing on archaea.

Among the with metagenomics newly revealed microorganisms are the members of the Asgard superphylum. A group of archaea that received great attention after the discovery of their role in bridging the gap between prokaryotes and eukaryotes. Asgard archaea are one of our target organisms.

One interesting novel cultivation technique is called reversed genomics. Here, with genomic data, antibodies are designed for the outer membrane regions of membrane proteins of our target microorganisms. When the antibodies stick to the proteins, they become fluorescent and with cell sorters that use a laser, the fluorescent cells will be sorted from the community.

Aim

In this project there is room for students to do a bioinformatical project, where metagenomic and metatranscriptomic data will be analysed to reconstruct genomes from community and to look at the activity of the community members. Next to that it is possible to focus on the antibody design for reversed genomics. There is also a possibility to do a wet lab project, where the student can focus on cultivation and for example use reversed genomics to enrich cells. Depending on timing, a student could also do a combination of wet and dry lab experiments.

Techniques

• General cultivation techniques
• (Anaerobic) cultivation
• Cell sorting
• Flow cytometry
• Sequencing
• Bioinformatics techniques
• Microscopy

BSc/MSc theses

Thesis projects are available for BSc or MSc students with interest in microbial cultivation, microbial ecology and bioinformatics. Please contact me via the contact form.