DOE JGI extended and updated the content of IMG and IMG/M recently as this linked press release shows (here is another), so today I’d like to just make a quick post to highlight that OpenHelix has a tutorial on IMG/M that is sponsored by JGI and thus free.
Metagenomics is a huge new field and IMG/M has some excellent tools and data!
Just saw in today’s GenomeWeb Daily News email that the Joint Genome Institute has announced its sequencing plans for 2009. It includes both genomes and metagenomes. You can read the GenomeWeb Daily News article, or the whole JGI announcment of projects which, according to JGI Director Eddy Rubin:
”The scientific and technological advances enabled by the information that we generate from these selections promise to take us faster and further down the path toward clean, renewable transportation fuels while affording us a more comprehensive understanding of the global carbon cycle”.
I for one am looking forward to exploring the new information as soon as it is available in IMG and IMG/M!
Metagenomics, which is really a new area of study (barely this last decade) in comparison to most biological areas of research, is already making into the mainstream press. The New York Times has an article yesterday entitled “Bacteria thrive in the inner Elbow, No Harm Done” (you’ll need a free registration to read that). The article quotes from metagenomic studies that show that our inner elbows contain a unique microbiome of species even in comparison to our upper arm, though it goes a more into metagenomic studies than just that. As the article states:
The research is part of the human microbiome project, microbiome meaning the entourage of all microbes that live in people.
The project is an ambitious government-financed endeavor to catalog the typical bacterial colonies that inhabit each niche in the human ecosystem.
That’d be this project. The article does a decent job of explaining why this project is helpful, but doesn’t really explain how this approach of metagenomics is different or how it’s done (in fact, it never says the word “metagenomics“). Oh well, can’t have everything.
For your edification: There is last year’s report “The New Science of Metagenomics” from the National Research Council (you can read free online, or purchase as a book. Also, of course there are at least two extensive databases of metagenomic data, IMG/M (free tutorial) and Camera.
Wow, how can you resist blogging about an article who’s title begins “Dissecting biological ‘‘dark matter’’…”? I found the article while working on a new ‘sponsored’ (read ‘free’) tutorial on the Integrated Microbial Genomes with Microbiome Samples (or IMG/M) resource. (I’m hoping the tutorial will be released in the near future & I’ll post when it is available.) IMG/M is a microbial resource that specializes in the analysis of metagenomes. Metagenomes are becoming hot – we’ve blogged about them in the past, as have lots of others. According to the article I found, “biological dark matter” refers to our paltry knowledge & understanding of the Earth’s microbial diversity. The article reports a method for isolating individual bacterial cells from the microbiome of the human mouth, but for my contribution to understanding microbial diversity, I want to give you a tip on using the IMG/M resource to select protein families in genomes based on their relative abundance. Click the image above to view the tip, or follow the links in this post to learn more on your own.
Marcy, Y., Ouverney, C., Bik, E.M., Losekann, T., Ivanova, N., Martin, H.G., Szeto, E., Platt, D., Hugenholtz, P., Relman, D.A., Quake, S.R. (2007). Inaugural Article: Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proceedings of the National Academy of Sciences, 104(29), 11889-11894. DOI: 10.1073/pnas.0704662104
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