Nature Reviews Microbiology 10, 599-606 (September 2012) | doi:10.1038/nrmicro2850
FOCUS ON: Next-generation sequencing
High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity
Nicholas J. Loman1, Chrystala Constantinidou1, Jacqueline Z. M. Chan1, Mihail Halachev1, Martin Sergeant1, Charles W. Penn1, Esther R. Robinson2 & Mark J. Pallen1 About the authors
Here, we take a snapshot of the high-throughput sequencing platforms, together with the relevant analytical tools, that are available to microbiologists in 2012, and evaluate the strengths and weaknesses of these platforms in obtaining bacterial genome sequences. We also scan the horizon of future possibilities, speculating on how the availability of sequencing that is 'too cheap to metre' might change the face of microbiology forever.
In bacteriology, the genomic era began in 1995, when the first bacterial genome was sequenced using conventional Sanger sequencing1. Back then, sequencing projects required six-figure budgets and years of effort. A decade later, in 2005, the advent of the first high-throughput (or 'next-generation') sequencing technologies signalled a significant advance in the ease and cost of sequencing2, delivering bacterial genome sequences in hours or days rather than months or years. High-throughput sequencing now delivers sequence data thousands of times more cheaply than is possible with Sanger sequencing. The availability of a growing abundance of platforms and instruments presents the user with an embarrassment of choice. Better still, vigorous competition between manufacturers has resulted in sustained technical improvements on almost all platforms. This means that in recent years our sequencing capability has been doubling every 6–9 months — much faster than Moore's law.