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[Bioinformatics Project] Comparative genomic analysis of bacteriophages against Gram-negative superbugs

Primary supervisor



  • Prof Jian Li
  • Dr Yan Zhu

Multidrug resistance (MDR) poses critical challenges to global health. In 2017 the World Health Organization identified Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacteriaceae as the top-priority pathogens that urgently require development of novel therapeutic options. Recently, bacteriophage therapy has attracted extensive attention owing to its potential of being used as novel antimicrobials to combat MDR pathogens.

Bacteriophages are the most abundant and diverse organisms in the biosphere. To date, there are approximately 10,000 complete phage genomes in the GenBank database. Despite their relatively small genomes, bacteriophages show impressive genomic diversity and complex evolutionary relationships that do not follow traditional hierarchical phylogeny. The limited understanding of phage genomes and evolutionary relationship has significantly hindered the development and optimisation of effective bacteriophage therapy against ‘superbugs’.

This project will conduct comparative genomic and evolutionary analyses of bacteriophages infecting top-priority Gram-negative pathogens. The available bacteriophage genomes from public databases will be combined with our own sequenced genomes for comprehensive analysis. Evolutionary analysis for core genes will be conducted and compared with the phylogeny of host bacteria to investigate the bacteriophage-bacteria interactions in the context of coevolution.


For more information, contact the primary supervisor Prof Jian Li <>

Student cohort

Double Semester


This project aims to construct the evolutionary relationship of bacteriophages infecting top-priority Gram-negative ‘superbugs’ using comparative genomics.

Required knowledge

The student should have:

  • extensive experience in R, python and Linux shell programming.
  • basic bioinformatics knowledge (e.g. blast, multi sequence alignment, phylogenetic tree construction) will be ideal.