| Abstract
Sequencing microbial genomes provides a comprehensive understanding that no other method can provide. For example, it is now possible to achieve single base resolution of the bacterial chromosome, and detailed sequence of all extrachromosomal elements, including plasmids and phages. Improvements in next-generation sequencing methods now enable routine whole bacterial genome sequencing in a single day. Assembling the genome from sequencing reads can be easily performed on a desktop computer, allowing high resolution classification of bacterial subtypes. Many important features, including resistance, virulence, and pathogenicity, can be examined simultaneously with high accuracy. In addition to genomic experiments, next-generation sequencing can be used to analyze the complete transcriptome of microbes for interpretation of gene structure and regulation. Sequencing complex microbial populations or metagenomes provides a comprehensive census of species within samples, including those that cannot be cultured or phenotyped. Subtle changes in microbial populations resulting from, or predictive of, changes in the health status of a patient can be assessed easily and accurately with next-generation sequencing. |
Jonathan Eisen's Lab 