1 Insights on Biology and Evolution from Microbial Genome Sequencing

Abstract

During the past 10 years, genomics-based approaches have had a profound impact on the field of microbiology and our understanding of microbial species. Since the first report on the complete genome sequence of Haemophilus influenzae in 1995 (Fleischmann et al. 1995), nearly 300 other prokaryotic genome sequences have been completed (http://www.genomesonline.org/; http://cmr.tigr.org/tigr-scripts/CMR/CmrHomePage.cgi), with another 750 projects underway. In the early days of microbial genomics, our ignorance about the extent of species diversity was reflected in the assumption that the complete sequence of 20–30 carefully chosen representatives of the bacterial and archaeal domains of life would provide a sufficient amount of information for follow-up investigations. As sequence data began to accumulate, it quickly became clear that we had underestimated the wealth of genetic and biochemical diversity in the prokaryotic world. Indeed, the completion of the sequence of Escherichia coli O157:H7 by Perna and colleagues in 2001 revealed that this new isolate contained more than 1300 strain-specific genes as compared with E. coli K-12. These genes encode proteins involved in virulence and expanded metabolic capabilities, as well as several prophages. This was a striking example of the fact that two members of the same species could differ in gene content by almost 30%. Today, many genomics efforts are focused on sequencing multiple isolates and strains and providing new insights into species diversity and the dynamic nature of the prokaryotic genome.

Because of their larger genome sizes, genome sequencing efforts on fungi and unicellular eukaryotes were slower to get started than projects...