My experience with metagenomics thus far

The techniques of metagenomics first came to my attention in 2005 during my honours year. My project involved trying to identify uncultured small volume viral communities associated with corals using sequence information without a priori sequence knowledge and thus it was natural that i should become aware of metagenomics.

Unfortunately this awareness came too late to help me in honours and I persevered using random PCR cloning and sequencing techniques.

In the first year of my PhD, I was fortunate enough to spend 6 weeks working in one of the pioneering labs in the field at San Diego State University in California (http://phage.sdsu.edu/) where i learnt the techniques necessary to acquire and process viral metagenomic samples (as well as working with some great people). On my return to Flinders University I spent several months setting up the equipment and processes necessary to conduct the work here.

After several fluctuations of application my PhD. has settled on using metagenomics (supported by more traditional molecular techniques) to investigate how microbial and viral communities adapt to changes in salinty along a natural gradient in the Coorong lagoon, South Australia. The Coorong ranges from seawater to hypersaline and encompasses environments that may be considered 'ancient' as well as 'futuristic' given the major influence of climate change on salinity levels.

I am currently preparing to sequence my first samples using a GS-FLX 454 Pyrosequencer (Roche) and am engaged in sample quality control to ensure that the significant amount of money required is money well spent.

As more and more publications and datasets become available I'm constantly reminded of the power of metagenomics when applied wisely (especially when using high throughput sequencing). The ability to be able to view whole communities within the metabolic context of their environment in a single dataset when coupled to the high throughput nature of metagenomics will revolutionise how we view the structure and evolution of genetic sequence diversity in the biosphere.

I just want my own datasets to analyse!

Tom