My work is focused on a culture-independent pipeline for the targeted access and the subsequent functional genome characterization of bacterial species from the environment.
This pipeline combines fluorescence in situ hybridization (FISH) with fluorescence activated cell sorting (FACS) and subsequent whole genome sequencing. A taxon-specific FISH probe hybridizes to the target cells which are subsequently enriched by cell sorting based on the fluorescence signal. Finally, the DNA of the sorted cells is amplified and sequenced. Due to the reduced diversity within the sequences, genome assembly is facilitated and we retrieve metagenome assembled genomes (MAGs) from the targeted group. Genome annotation of these MAGs provides insights into the functional potentials.
The development of the pipeline involved an optimization of the recently developed hybridization chain reaction (HCR)-FISH method and the assessment of various cell fixatives concerning their influence on HCR-FISH signal intensity and the quality of genome sequencing and assembly.
The application of this pipeline on planktonic seawater samples from the North Sea enabled the description of a novel candidate species which has not been cultivated to date.