E-Poster Presentation Australian Society for Microbiology Annual Scientific Meeting 2021

Network Phylogeny: Serratia Phages in a Sea of Sequences (#247)

Beau J Patrick 1 , Steven Batinovic 1 , Hiu Tat Chan 1 , Cassandra Stanton 1 , Steve Petrovski 1
  1. Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, VIC, Australia

The evolution of a framework capable of providing predictive, informative and explanatory classifications of bacteriophages (phages) has been a laboured process. This is due, in part, to the complexities incorporated by horizontal gene transfer into phage genomes. An influx of genomic data from phage studies has overwhelmed public databases that rely on outdated methods of phage classification. Widespread recognition of the need for contemporary methods has prompted global discussion regarding how to classify phages in a way that is scalable and that incorporates phages true evolutionary histories. We isolated six novel phages infecting the pathogenic species Serratia marcescens and investigated their genetic relationships by performing a contemporary framework. The Serratia marcescens phages were consolidated with existing Serratia phages into clusters of related genomes, where 20 out of the 32 phage sequences could be clustered together with at least one other. Nucleotide sequence similarity, genome synteny analysis and marker gene phylogeny all support these as being genetically related lineages. Network phylogeny program vConTACT2 facilitated gene content analysis of the Serratia phages against a reference database of 2272 phage genomes. Subsequently, a reticulated network phylogeny was generated displaying phages within a network of interrelated viral clusters. This allows visualisation of phage relatedness at the protein coding level and places the Serratia phages in context amongst the global phage sequence space. Interestingly, relationships not previously revealed by nucleotide sequence similarity and marker gene phylogeny were visible. This highlights the inability of traditional approaches to account for the high gene transfer and nucleotide sequence divergence rates characteristic of phages.