title: Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy.
abstract: 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.
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany.
authors.forename: Jan P
authors.initials: JP
authors.lastname: Meier-Kolthoff
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany.
authors.forename: Richard L
authors.initials: RL
authors.lastname: Hahnke
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany.
authors.forename: Jörn
authors.initials: J
authors.lastname: Petersen
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany.
authors.forename: Carmen
authors.initials: C
authors.lastname: Scheuner
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany.
authors.forename: Victoria
authors.initials: V
authors.lastname: Michael
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany.
authors.forename: Anne
authors.initials: A
authors.lastname: Fiebig
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany.
authors.forename: Christine
authors.initials: C
authors.lastname: Rohde
authors.affiliation: Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany.
authors.forename: Manfred
authors.initials: M
authors.lastname: Rohde
authors.affiliation: LGC Genomics GmbH, Ostendstraße 25, 12459 Berlin, Germany.
authors.forename: Berthold
authors.initials: B
authors.lastname: Fartmann
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, Ca, USA.
authors.forename: Lynne A
authors.initials: LA
authors.lastname: Goodwin
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, Ca, USA.
authors.forename: Olga
authors.initials: O
authors.lastname: Chertkov
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, Ca, USA.
authors.forename: Tbk
authors.initials: T
authors.lastname: Reddy
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, Ca, USA.
authors.forename: Amrita
authors.initials: A
authors.lastname: Pati
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, Ca, USA.
authors.forename: Natalia N
authors.initials: NN
authors.lastname: Ivanova
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, Ca, USA.
authors.forename: Victor
authors.initials: V
authors.lastname: Markowitz
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, Ca, USA ; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, Ca, USA.
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany.
authors.forename: Markus
authors.initials: M
authors.lastname: Göker
authors.affiliation: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany.
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Klenk
keywords: Clustering; DNA:DNA hybridization; G+C content; GBDP; OPM; Phenotype; Phylogenomics; Phylotypes; Supermatrix