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Although  Escherichia coli  is the most widely studied bacterial model organism and often considered to be the model bacterium  per se , its type strain was until now forgotten from microbial genomics. As a part of the   G   enomic   E   ncyclopedia of   B   acteria and   A   rchaea  project, we here describe the features of  E. coli  DSM 30083 T  together with its genome sequence and annotation as well as novel aspects of its phenotype. The 5,038,133 bp containing genome sequence includes 4,762 protein-coding genes and 175 RNA genes as well as a single plasmid. Affiliation of a set of 250 genome-sequenced  E. coli  strains,  Shigella  and outgroup strains to the type strain of  E. coli  was investigated using digital DNA:DNA-hybridization (dDDH) similarities and differences in genomic G+C content. As in the majority of previous studies, results show  Shigella  spp. embedded within  E. coli  and in most cases forming a single subgroup of it. Phylogenomic trees also recover the proposed  E. coli  phylotypes as monophyla with minor exceptions and place DSM 30083 T  in phylotype B2 with  E. coli  S88 as its closest neighbor. The widely used lab strain K-12 is not only genomically but also physiologically strongly different from the type strain. The phylotypes do not express a uniform level of character divergence as measured using dDDH, however, thus an alternative arrangement is proposed and discussed in the context of bacterial subspecies. Analyses of the genome sequences of a large number of  E. coli  strains and of strains from > 100 other bacterial genera indicate a value of 79-80% dDDH as the most promising threshold for delineating subspecies, which in turn suggests the presence of five subspecies within  E. coli .   Electronic supplementary material  The online version of this article (doi:10.1186/1944-3277-9-2) contains supplementary material, which is available to authorized users.

Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy