PhD Projects » ESR 5: Bacteriophage–host relationships prediction

Host institution:Helmholtz Zentrum München (HMGU), Germany
Local supervisor:Dr. Li Deng (HMGU, Institute of Virology)
Local co-supervisor:Prof. Dr. Caroline Friedel (Ludwig Maximilians University Munich, Institute for Bioinformatics)
Project partner:ESR 10

This project seeks to understand how (bacterio-)phages are functionally linked to their Bacteria or Archaea hosts both using experimental and bioinformatics approach. Phage identified using cultivation-independent viral metagenomic sequencing lack sequence similarity to any of previously sequenced ones can hardly be assigned to their hosts. Different methods exist to predict hosts for phage sequence, e.g. single or multiple features (co-abundance, sequence homology, similarity to other phages or sequence composition similarity between phages and their hosts) or using these features in machine learning models.

Therefore, we aim to integrate features of our unique experimental identified, host-linked viral metagenomic data in a deep learning model to improve the prediction performance.

  • Development of a modified version for experimentally linking phages to their anaerobic bacteria and archaea hosts based on the previously published culture-independent viral-tagging (VT) method for aerobic bacteria-phage pairs. In this single cell viral tagging approach, virions from an environmental sample are fluorescently labelled through DNA staining and upon them infecting host cells, the infected host is labelled. This is followed by single cell sorting via FACS of the infected hosts together with the phages infecting. We plan to use three bacterial strains (complete genome available) to VT the same 20 water samples to create 60 VT metagenomic datasets, as well as 20 community viral metagenomics datasets.
  • Metagenomic sequencing of the specific phage communities on selected bacteria and archaea hosts as both bulk level and single cell level.
  • Single phage-host screening, isolation and sequencing based on selected gene markers representing different adsorption or infecting strategies (together with ESR 10).
  • Study the adsorption and host recognition mechanisms of the newly isolated phages.
  • Generation of viral-tagged metagenomes on the same selected bacteria and archaea hosts in contaminated groundwater ecosystems, and community co-occurrence microbiomes and viromes in the same ecosystems (together with ESR 10 and BioRelate).

Doctorate will be awarded at Technical University of Munich.