Genome Mining and expression profiling of intestinal commensals

For this research project, Mrs Noora OTTMAN has been recruited.

Main supervisor

University of Wageningen (H. Smidt)

Start date : beginning of 2011

Objective. Functional (meta-)genomics to elucidate functionality of novel intestinal isolates, with special focus on interaction with mucosal barrier.

Approach. The genome sequences of Victivallis vadensis and Akkermansia muciniphila have recently become available. In addition, metagenomic libraries can be enriched for corresponding genomic fragments, further expanding available sequence data. A. muciniphila is dedicated to the degradation of mucin. This allows for (1) building genome based metabolic models, (2) in vitro versus in situ gene expression profiling, (2) cross talk in vivo analyses (germ free and conventional models), (3) differential in vivo & in vitro metabolic predictions, (3) 13C based metabolic in vitro and in situ profiling using germ free animals.

Deliverables - Available soon