Bioinformatics of Microbial Sequences

The pioneering work of Carl Woese demonstrated that comparison of biological sequences is the key to inferring evolutionary relationships and population structures in the microbial biosphere. These studies clearly showed that the great majority of the biodiversity on this planet is microbial. Since the determination of the first bacterial genome sequence in 1995, the genomics revolution has added great detail to the understanding of bacterial evolution and gene flow. One issue that is subject to on-going research and debate is whether lateral gene transfer has an effect on population structures, and whether evolutionary relationships between bacteria may be best regarded as a tree or a network. Recent efforts to sequence genomes from multiple strains within individual bacterial species have revealed that in general any given bacterial clone contains only a subset of the gene content of the species. A typical bacterial genome is composed of a core set of genes that are shared by all strains in the species, and accessory genes that are mobile, and often confer clinically significant properties. The immense and rapidly expanding quantity of genome sequence information has made it possible for DNA-based diagnostic and typing methods to be designed with precisely understood performances in relation to the population structure of the species or the likely gene content of an analytical sample. � 2010 Springer-Verlag New York.