April 1st, 2015
We know that we are surrounded by a myriad of microorganisms, but precise characterization of the diversity of this microscopic population was still impossible recently. The difficulty of identifying and characterize microbes in samples arise from the fact that the different conditions used in laboratories to grow microbes are unsuitable for a majority of them. These hard to know microorganism became known as ‘microbial dark matter’, because they were as hard to get a handle on as the dark matter in the universe.
Until recently, determining a genome’s sequence required many copies of the DNA, and thus only microbes grown in the lab could be sequenced, but a novel technique can determine DNA from a single cell.
This technique is based on a new amplification method, developed by Professor Xiaoliang Sunney Xie’s group at Harvard University and reported in the December 21, 2012, issue of Science. It reduces bias resulting from existing methods that use exponential amplification. Known as multiple annealing and looping-based amplification cycles (MALBAC), this technique employs special primers to initiate the amplification process, allowing the DNA to be copied in a non-exponential way. (Primers are short strands of complementary DNA molecules that bind to the DNA template and act as a starting point for the synthesis of new DNA.)
Through the use of special primers in MALBAC, the genomic DNA is amplified to form loops that can’t act as templates for further replication. Due to the formation of these amplified loops, only the initial genomic DNA can be copied in each cycle, resulting in a near linear amplification of the original DNA. This pre-amplification process reduces much of the sequencing bias present in existing methods.
Already 200 new microbes have been identified using the MALBAC technique. By filling out the microbes family tree, it will now be easier for researchers to work with DNA collected from the environment, because they have more reference DNA to compare it to. Also, this information could help to figure out how to grow some of these microbes in the lab and study them further.
Roseanne F. Zhao, Ph.D. (2013). The Power of Sequencing Single Cell Genomes
NIH Medical Scientist
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