Darwin's Birthday

Happy Birthday Charles Darwin!

for a couple of cool posts about this checkout:

http://phylogenomics.blogspot.com/2009/02/10-simple-ways-to-honor-charlie-d-aka.html

http://phylogenomics.blogspot.com/2009/02/charles-darwin-relic-hidden-in-chimp.html


And if you want to buy a T-Shirt a friend of mine designed then check out this:

http://www.redbubble.com/people/delosangeles/t-shirts/2195771-12-200-years-of-darwin

Celebrate in style...like these guys:

http://www.bbc.co.uk/shropshire/content/articles/2009/02/02/darwin_beer_feature.shtml

Cheers

Tom

how time flies

Wow, i really should update this more often

I guess that's what happens when you are writing a PhD. thesis

So in the time since i last posted i have sequenced four metagenomes, been to a really good conference in Cairns and well, not written any blog posts

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

Welcome - First Post

Welcome!

This blog represents my initial attempt at stimulating discussion and collaboration between researchers in the metagenomics community in Australia.

Whilst all are welcome it is primarily aimed at postgraduate students doing metagenomics projects so as to allow people to get in touch and help each other out in an informal environment.

Australia's unique habitats and biodiversity offer a great deal to the field of microbial metagenomics (metagenomics also offers a lot to Australia's unique habitats and biodiversity), but due to a limited degree of infrastructure and funding the field has yet to become a major force in Australia. Having said this, people are realizing the potential and doing metagenomics (largely it seems with international collaborators) so the time is ripe for taking this field to the next level in this country. I believe the first step is stimulating dialogue between researchers using metagenomics techniques in Australia and to create a network of people willing to discuss, share and contribute ideas as to how metagenomics should be done and how it can benefit and advance microbial ecology and medicine in Australia.

As to how this will work, consider it a work in progress. If you do wish to be able to post please e-mail me (jeff0103@flinders.edu.au) and I can give you access. I am assuming at first it will just be me rambling about my work and maybe suggesting some references for interested readers but hopefully other people will join and we can go from there.

Cheers

Tom

Thomas Jeffries

PhD. Candidate

School of Biological Sciences

Flinders University

Adelaide

Australia

PS: what is metagenomics? Essentially metagenomics refers to the sequence based analysis of whole uncultured microbial and viral communities. Sequencing the meta-genome (that's a lot of genomes) in an environment and analyzing them in clever ways can provide information on the taxonomy, metabolism and ecological structure of the community and shed light on the relationship between microbes and their environment. A good starting point for more information is here: http://camera.calit2.net/metagenomics/what-is-metagenomics.php