Matthew Flinders Fellow in Marine Biology
College of Science and Engineering
My research uses genomics to investigate the biodiversity and ecology of microbes and viruses on coral reefs, kelp forest and shark epidermis. I am interested in understanding how microbial and viral function responds to environmental pressures and affects the health of the host and ecosystem. I have developed novel tools, undergraduate education programs and international workshops to analyze metagenomics data and understand the structure of host microbiomes. I demonstrated that the functional attributes of microbial and viral metagenomes could distinguish across biomes.
I have described that the microbial dysbiosis is driving degradation on coral reefs and showed that there is local genomic adaptation that occur to coral reef-associated microbiomes across natural gradients and with anthropogenic stress. The local adaptations lead to distinct biogeography and evolution of marine microbial taxonomy and function. My lab developed a model of the coral microbiome that includes the influence of temperature and microbial network and we will use model to predict changes in microbial communities with climate change.
I have explored unique environments, such as the skin of sharks and shown that the skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge. We are currently increasing the diversity of sharks in the analysis and linking the microbiomes to physiology of the organism.
I have expanded my research to describe the genomics of the host, through mitochondrial and genome skimming, and have sequenced the California sealion, the silky shark and a guitarfish. We are using proteomics and metabolomics to link the microbiome with the physiology and distribution of the host. My work is at the forefront of cutting-edge, next generation DNA sequencing, and I am interested in applying my skills to uncover the unique microbial diversity within Australia.
Bachelor of Science, Marine Biology and Zoology, James Cook University, 1992
Masters of Science, James Cook University, 2001
Doctor of Philosophy, James Cook University, 2005
I developed a course which introducted metagenomics and next generation DNA sequencing in 2010. The course has taught about 700 students both techniques associated with DNA sequenicng across four major platforms and the processes of annotating microbes. The students have investigate microbes on the skin of fish and sharks, the surface of algae including kelp and sargassum, and sea water and hypersaline environments. My experience has lead me to be involved in introducing bioinformatics into the life sciences across the USA. i will be developing these ideas and topics into Flinders University.
Flinders Accelerator for Microbiome Exploration (FAME): is a University-wide initiative to promote and enhance microbiome and metagenome studies across Flinders University, Adelaide, and South Australia. It is co-directed by Prof. Robert Edwards, the FAME Director of Bioinformatics and Human-Microbe Interactions, and co-directed by Prof. Elizabeth Dinsdale, the FAME Director of Environmental Microbiomes. We are looking forward to working with all groups that would like to understand how the microbiome is affecting their area of research. FAME is integral to this proposal and will provide scientific support for experimental design, sample collection, data generation (DNA sequencing), bioinformatics, and statistical analysis. Edwards and Dinsdale have published more than 100 microbiome and metagenome papers and have led this field for over 15 years.
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