INTRODUCTION

Despite our interest and motivation, bacteria are not particularly easy organisms to study; their niches are complex and poorly understood and the vast majority of these species are difficult to culture or to manipulate in the laboratory. Of all bacteria, it is pathogens whose physical, social, and economic impact on our day-to-day lives garners the most attention, from both scientists and non-scientists alike. As a result, pathogens are among the best-studied bacteria, and lessons we learn from them are often generalized to other, non-pathogenic bacteria. Not surprisingly, the first lessons learned in the so-called genomic era came from pathogens, which were the first organisms with fully sequenced genomes. The promise of genomics was that the limitations of conventional microbiology could be overcome by studies of genome sequences and careful analysis of the genes contained therein. Here we examine how genomics has shaped our understanding of microbial genome evolution and ask how extensible these lessons may be. Among the notions that attracted widespread attention was the finding that certain clusters of genes are specifically responsible for virulence and that these loci are often obviously of foreign origin, having been introduced by the then under-appreciated process of lateral gene transfer or LGT. Coming more than a decade after these findings, this volume is focused on the hugely influential role of LGT in the evolution of genomes, particularly those of pathogenic bacteria.