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

Standards in Genomic Sciences
Jan P Meier-KolthoffHans-Peter Klenk

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 ...Continue Reading

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Citations

May 29, 2019·Genome Biology and Evolution·Ana Paula AndreazzaLeda S Chubatsu
May 28, 2019·Systematic Biology·Jakub BarylskiEvelien M Adriaenssens
May 29, 2019·International Journal of Systematic and Evolutionary Microbiology·Carlos Cortés-AlbayayImen Nouioui
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Sep 7, 2019·International Journal of Systematic and Evolutionary Microbiology·Swapnil Doijad, Trinad Chakraborty
Aug 29, 2019·International Journal of Systematic and Evolutionary Microbiology·Imen NouiouiMichael Goodfellow
Jan 18, 2020·International Journal of Systematic and Evolutionary Microbiology·Joana RochaLuísa Peixe
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Datasets Mentioned

BETA
PRJNA50621
2528311135

Methods Mentioned

BETA
PCR

Software Mentioned

DELTRAN
BLAST
FastME
GGDC
RAxML
CRT
OrthoMCL
- CR
GBLOCKS
PAUP

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