Co-supervised by Dr Jennifer Boer (SHBS, RMIT) and Professor Katie Flanagan (UTAS).
The human gut is a vast reservoir of genetic potential and we are learning more and more how it relates to human health and disease. The new generation of deep metagenomic sequencing, consists in simultaneous sequencing of multiple microbial genomes at once and has provided us with a wealth of information on the composition of complex communities in our gut. As different microbial genomes can result in vastly different phenotypes and functions in our gut, it is critical to understand the genomic variations that characterize the different strains that are present.
We are currently working on a large-scale vaccine (DTP and influenza) human trial (n=600) in Tasmania in which we will map, as a world first, how innate immunity and innate training differs in humans based on age and sex, and how this affects responses to vaccines. We will be studying these aspects with a systems biology approach in which we will investigate whether the immunological changes in young and elderly are characterized with changes in the gut microbial composition.
Currently big data provided by metagenomics next generation sequencing (mNGS) is becoming a key driver for the advancement of precision medicine to personalize patient care. Therefore, to take full advantage of these complex datasets we will use bioinformatics to enable quicker and more comprehensive analysis.
Aims: By using a bioinformatics analysis pipeline we will investigate whether vaccination responses are affected by the microbiome profile, and whether it changes according to the vaccination sequence, or the age (young adults or elderly) or sex (male/female) of the vaccinees.
Hypotheses:
- DTaP vaccination modulates the microbiome, such as the influenza vaccine.
- Baseline non pathogenic microbiome profile effects will differ between younger adults and the elderly, and females compared to males.
Methods: Bioinformatics pipelines to analyse big volumes of metagenetic data. The analysis pipeline will roughly use packages such as trimomatic, FastQ screen, centrifuge/kraken and many more.
The PhD candidate: The preferred PhD candidate will have done an Honours or Masters in either immunology, or vaccines, microbiology, bioinformatics, biostatistics or a related discipline.
References: [1]. Chiu CY et al. Nat Rev Gen. 20 (2019):341 [2]. Noho-Konteh F et al. Clin Infect Dis. 63 (2016):1213 [3]. Fish E et al., Lancet. 387 (2016):1054
