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.

Author affiliations

  1. Nicholas J. Loman, Chrystala Constantinidou, Jacqueline Z. M. Chan, Mihail Halachev, Martin Sergeant, Charles W. Penn and Mark J. Pallen are at the Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK.
  2. Esther R. Robinson is at the Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford OX3 9DU, UK.

Correspondence to: Mark J. Pallen1 Email:

Published online 6 August 2012