Using the Core and Supra Genomes to Determine Diversity and Natural Proclivities among Bacterial Strains
Laura Nistico, Josh Earl, Luisa Hiller, Azad Ahmed, Adam Retchless, Benjamin Janto, J. William Costerton, Fen Z. Hu and Garth D. Ehrlich
from: Applications of Molecular Microbiological Methods (Edited by: Torben L. Skovhus, Sean M. Caffrey and Casey R.J. Hubert). Caister Academic Press, U.K. (2014)
The realization at the beginning of the current millennium that there are very substantial differences in gene content among the component strains of bacterial species together with the observation that there exists profound phenotypic heterogeneity amongst these strains led directly to the development of the field of comparative bacterial genomics, and the concepts of the core and supra (pan) genomes. The core genome is composed of the set of genes shared by all members of a given species (or other taxonomic grouping), and the supragenome is the set of all genes contained by the same grouping. Those genes not present in the core genome, but present in the supragenome, are referred to as distributed (accessory) genes, and it is this last group which is responsible for much of the intraspecies heterogeneity. In the current work we provide comparative genomic evidence for both the core genome hypothesis and the distributed genome hypothesis, and describe a testable means to determine if a strain or particular group of strains belongs within an extant genomically-defined species (or other taxonomic) grouping read more ...