Complete genome sequence of DSM 30083T, the type strain (U5/41T) 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 GenomicEncyclopedia ofBacteria andArchaea project, we here describe the features of E. coli DSM 30083T 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 30083T 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 materialThe online version of this article (doi:10.1186/1944-3277-9-2) contains supplementary material, which is available to authorized users.

Genome-Based Taxonomic Classification of Bacteroidetes

“…Furthermore, the G+C values calculated from the genomes of H. seregens and P. dentalis are almost identical, with 56.0 and 55.9%, respectively, even though this is not currently reflected in the species descriptions. Digital DNA:DNA hybridization between the genome sequences of H. seregens ATCC 51272 T and P. dentalis DSM 3688 T conducted with the recommended settings of the GGDC yielded 87.40 ± 2.36% DDH similarity and thus indicated identical species, even identical subspecies (Meier-Kolthoff et al, 2014b). We conclude that H. seregens is a later heterotypic synonym of P. dentalis .…”

Genotyping ofBartonellabacteria and their animal hosts: current status and perspectives

“…A threshold of 70% hybridization has been used as the 'gold standard' criterion for distinguishing new bacterial species (Tindall et al 2010); however, this technique requires the use of cultured isolates, specialized equipment and multiple confirmatory tests due to variation across experimental runs. Alternative genome-wide distance measures included average nucleotide identity (Konstantinidis and Tiedje, 2005;Konstantinidis et al 2006;Goris et al 2007;Richter and Rosselló-Móra, 2009) and digital DNA-DNA hybridization (Auch et al 2010;Meier-Kolthoff et al 2014a, b). One considerable advantage of these techniques is that they do not necessarily require cultured isolates and can be calculated from draft genomes assembled from metagenome and transcriptome sequencing.…”

Blastococcus capsensis sp. nov., isolated from an archaeological Roman pool and emended description of the genus Blastococcus, B. aggregatus, B. saxobsidens, B. jejuensis and B. endophyticus

“…Phylogenetic analyses and rooting of the inferred tree were conducted as previously described (Montero-Calasanz et al, 2013) using the DSMZ phylogenomics pipeline (Meier-Kolthoff et al, 2014) adapted to single genes integrated in the GGDC web server (MeierKolthoff et al, 2013a) available at http://ggdc.dsmz.de/. Pairwise similarities were calculated as recommended by Meier-Kolthoff et al (2013b) for the 16S rRNA gene available via the GGDC web server.…”