Leicester Microbial Sciences and Infectious Diseases Centre (LeMID)

Phage genomics

Phage genomics is the study and function of bacteriophage genomes.

This is achieved by the sequencing of phage isolates, identification of prophages within bacterial genomes or through metagenomics. 

Metagenomics is the study of all genomes within a sample and does not require culturing of the organisms of interest. This is of great use in the study of phages, where the majority of the hosts they infect have not been cultured yet, so the phages themselves cannot be cultured.

Viral metagenomics is simply the viral genomes within a sample (often dominated by phages), which is achieved by the use of filtration to remove bacteria and larger organisms prior to DNA extraction. It allows the identification of phage genomes within an environment without the need for culturing.

Researchers at Leicester are studying phage genomics on a variety of systems, including C. difficile, Salmonella, Escherichia coli , Vibrio spp, Pseudomonas, Helicobacter and Cyanobacteria.

By using comparative genomics researchers trying to understand the diversity of genes phage carry and how this alters infection. This ranges from marine cyanophages where they are studying the “cargo” genes that phage carry that can alter host metabolism by shutting down CO2 fixation, but maintain photosynthesis. This process is important in biogeochemical cycling as the oceans produce ~ 50% of the oxygen we breathe. Cyanobacteria ( the host of cyanophages) are the most abundant CO2 fixing (02 producing) primary producers in the oceans. To vibriophages that carry antibiotic resistance genes.

We are also studying vibriophages and their diversity, in particular we have focused on what “cargo” genes vibriophages carry and how they might spread the transfer of antibiotic resistance genes.

Researchers are also studying phage genomics that can be used to create phage cocktails for the treatment of a number of infections. Professor Martha Clokie's lab is developing phage cocktails to be used in animal feeds with Dr Millard's group using genomics and engineering to create phages that are more efficient at killing their hosts.

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