Genome Sequencing of Unculturable Bacteria


Conventional DNA sequencing of a microbial genome usually entails extracting sufficient DNA from a culture grown up from a single bacterium; however, most microbes from natural environments do not have established laboratory culture conditions and, therefore, pose a challenge in providing enough DNA. This includes many strains of the most prevalent photosynthetic marine microbe, Prochlorococcus, which have major roles in carbon cycling and fixation. In the June 2006 issue of Nature Biotechnology, Dr. George Church led a GTL-funded team of MIT-Harvard Medical School scientists, in developing a new strategy that allows high-fidelity amplification of DNA from a single cell. The breakthrough comes from using DNA-digesting enzymes to cut away undesirable branched DNA structures that tend to form during early rounds of DNA amplification, leaving only linear DNAs to be tremendously amplified and subsequently sequenced. This technique allowed the genomic sequence to be obtained from a single Prochlorococcus microbe, and opens a window to obtain genomic information from individual members in complex microbial communities.


Kun Zhang, Adam C. Martiny, Nikos B. Reppas, Kerrie W. Barry, Joel Malek, Sallie W. Chisholm & George Church, (2006) Sequencing genomes from single cells by polymerase cloning, Nat. Biotech 24 (6): 680-686.