A really important technique for metagenomic studies: stable isotope probing

Another really interesting microbial diversity paper in mBio.  This one is from Josh Neufeld and colleagues: Multisubstrate Isotope Labeling and Metagenomic Analysis of Active Soil Bacterial Communities.

The key thing they did is summarized in their abstract:

We incubated samples from three disparate Canadian soils (tundra, temperate rainforest, and agricultural) with five native carbon (12C) or stable-isotope-labeled (13C) carbohydrates (glucose, cellobiose, xylose, arabinose, and cellulose). Indicator species analysis revealed high specificity and fidelity for many uncultured and unclassified bacterial taxa in the heavy DNA for all soils and substrates.

And then they sequence metagenomes from the samples and use the labelled carbon to separate out the DNA from active cells versus from inactive cells.  It is a method that has been used a few times in prior studies and this is one of the better examples I have seen.  Definitely worth a read for those thinking about going beyond just sequencing and learning about function in communities.

stable isotope probing

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Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. My lab is in the UC Davis Genome Center and I hold appointments in the Department of Medical Microbiology and Immunology in the School of Medicine and the Department of Evolution and Ecology in the College of Biological Sciences. My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis (see my lab site here which has more information on lab activities).  In addition to research, I am heavily involved in the Open Access publishing and Open Science movements.