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Human microbiome research projects

A novel bioinformatic tool for identifying plasmids and their hosts within the human microbiome

Ms. Georgina H. Joyce

Plasmids are mobile extrachromosomal genetic units hosted by microorganisms that behave as a vessel for the sampling of potentially advantageous traits from a population’s gene pool. This project aims to further optimise a prototype novel bioinformatic tool, RecurM, developed by Daniel Rawlinson at the Australian Centre for Ecogenomics in 2019. Unlike previous approaches, this tool does not rely on reference databases to identify a plasmid.

This project trials RecurM on metagenomic datasets supplied by the Integrative Human Microbiome Project (HMP), which investigated host-microbiome dynamics over the course of inflammatory bowel disease. The output of RecurM are clusters that may represent a plasmid. Clusters associated with disease or in high abundance within the dataset will be characterised using EnrichM, and associated with a likely host.

The ideal outcome of this project is to optimise RecurM so that it is user-friendly for public use. From the HMP dataset, it is expected that novel plasmids associated with disease will arise from the use of RecurM. Their characterisation and association with their microbial host will provide a starting point not only for further understanding the role of plasmids within complex biological environments but also for characterising inflammatory bowel disease dysbiosis.

Alongside the ongoing advancement of deep sequencing technologies is the generation of an enormous amount of genetic data which require bioinformatic tools to efficiently investigate. Despite their key role in microbial evolution and the spread of antibiotic resistance, the difficulty in identifying plasmids bioinformatically in metagenomic datasets means that they are typically overlooked in these studies. The development of a reference-free bioinformatic approach to plasmid discovery is foreseen to contribute significantly to understanding their role in microbial ecology.