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Unlocking the potential of bacterial genomes

Analysing the genomes from bacteria species helps us to understand their evolution, and that in turn allows us to find innovative ways to use them in our health, conservation and agricultural sectors.

Globally, researchers are interested in horizontal gene transfer (HGT) - the movement of genes between organisms other than by DNA inherited from parents, which is an important factor in the evolution of many organisms. HGT is common in bacterial species, and research that helps to better understand why and how this process occurs can be used to predict microbial responses – anything from environmental shocks like the addition of fertilisers in soil or like antibiotic responses in hospitals.

David Waite

Postdoctoral fellow David Waite

Genomics Aotearoa Postdoctoral Fellow David Waite joined the Environmental Metagenomics team to continue his interest bacterial genomes. In particular, he’s interested in better classification of bacterial systems to help the process.

By sequencing and reconstructing bacterial genomes from carefully selected environments, David’s hoping to further explore the role of HGT amongst bacteria. He wants to understand the forces which limit its potential.

“I am also involved in developing several novel pipelines for reconstructing non-bacterial genomes, and hope to contribute towards the development of genomic capability in New Zealand by creating new analytical tools.”

David’s career so far

David’s Honours and PhD research with Professor Mike Taylor at the University of Auckland focused on the microbial organisms associated with the critically endangered kakapo. The aim was to understand the ecology and natural variability of bacterial communities found in the gut of kakapo, and to identify the impact of human intervention.

Then he worked on molecular tools for rapid identification of high priority invasive species for the Ministry for Primary Industries. “A constant research interest was the flexibility of bacterial genomes, and the consequences this has on our ability to model microbial systems. This issue partially stems from poor classification of bacterial species, meaning a problematic record of HGT.”

Keen to contribute to resolving this ambiguity amongst bacteria, David took on a postdoctoral fellowship at the University of Queensland as part of the Genome Taxonomy Database (GTDB) project. “This provided a powerful platform to resolve evolutionary differentiation between microbial species; in one project we were able to recognise a large number of apparently horizontal gene transfer events between Epsilonproteobacteria and phylum Aquifae were in fact vertical evolution between two related bacteria.”

David’s areas of expertise:

  • Genome assembly
  • Recovery of genomes from metagenomic data
  • Phylogenomic analysis
  • Machine learning and validation
  • Pangenome analysis