Unculturable Bugs Yield To Genome Sequencing

Getting enough DNA for genome sequencing is a challenge with organisms that are difficult to grow in culture. A team of Harvard geneticists led by postdoc Kun Zhang and professor George M. Church eliminated the need for culturing by improving an enzymatic amplification method used to generate copies of the DNA in single cells (Nat. Biotechnol., published online May 28, dx.doi.org/10.1038/nbt1214).

Because background DNA contamination can be a problem, they used a fluorescent dye to monitor the amplification in real time, enabling them to quantify and subsequently eliminate most of the background. They also discovered that the amplification method generates hyperbranched DNA. They reduced the branching with a three-step enzymatic treatment.

Using the method, they sequenced the genomes of individual cells of lab strains of Escherichia coli and Prochlorococcus (a common bacterium found in the ocean), as well as “wild” Prochlorococcus. They plan to use the technique to sequence individual human chromosomes as well.