PROJECT INFORMATION
GOLD Project ID
Gp0007996  
Project Name
Escherichia coli O1:K1:H7 U5/41, DSM 30083  
Other Names
  
Legacy ER Project ID
17781  
Legacy GOLD ID
Gi07590  
NCBI BioProject Name Escherichia coli DSM 30083 = JCM 1649 = ATCC 11775
NCBI BioProject ID 50621
NCBI BioProject Accession PRJNA50621
NCBI Locus Tag
Escco  
NCBI BioSample Accession SAMN00718807
PI Hans-Peter Klenk
Added By Ionna Pagani on 2010-09-02
Last Modified By Hema Katta on 2018-12-20
Project Comments
  
Project Status
Permanent Draft  
Project Relevance Poultry Pathogen
Bioenergy
Comparative analysis
Biotechnological
GEBA
Sequencing Center DOE Joint Genome Institute (JGI) (USA)
Collaborating Institute Leibniz Institute (Germany)
Funding Agency U.S. Department of Energy (DOE) (USA)
Project Description
As a part of the GenomicEncyclopedia ofBacteria andArchaea project, we here describe the features of E. coli DSM 30083 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 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.  
Is JGI Project
Yes  
Project Information Visibility Public
PROJECT TYPE
Specimen Organism
Nucleic Acid DNA
Sequencing Strategy
Whole Genome Sequencing  
EXTERNAL PROJECT LINKS
JGI Portal Download Raw Sequence Data
Project Information
  
Database
  
Genome Publications Standards in genomic sciences 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.

Other Publications
  
SRA Experiment
  
PROJECT COMPOSITION
Study A Genomic Encyclopedia of Bacteria and Archaea (GEBA)
Organism Escherichia coli O1:K1:H7 U5/41, DSM 30083
Analysis Projects Escherichia coli O1:K1:H7 U5/41, DSM 30083
Number of Analysis Projects 1
Number of DAPs
0  
SEQUENCING INFORMATION
Sequencing Status Complete
Sequencing Quality (MIGS-31) Level 3: Improved-High-Quality Draft
Finishing Goal
  
Sequencing Comments
  
Sequencing Technology (MIGS-29) Illumina GAIIx
454 GS FLX Titanium
Library Method (MIGS-28)
  
Number Of Reads
  
Read Size
5038133  
Vector
  
GC Percent
51  
Chromosome Count
1  
Plasmid Count
1  
ORGANISM NAME
GOLD Organism ID Go0007996
Organism Name
Escherichia coli O1:K1:H7 U5/41, DSM 30083  
Other names (alias, synonyms, short names, common names)
  
Organism Domain
BACTERIAL  
Phylogeny
PROTEOBACTERIA-GAMMA  
Genus
Escherichia  
Genus Synonyms
  
Species
Escherichia coli  
Subspecies
  
Species Synonyms
  
Strain
U5/41  
Strain Synonyms
  
Serovar/Cultivar
O1:K1:H7  
Culture Collection ID
DSM 30083  
Type Strain
Yes  
Exemplar DOI
10.1601/ex.3093  
Exemplar Name
Escherichia coli  
Taxon DOI
10.1601/tx.3093  
Biosafety Level
2  
Organism Comments
  
Cultured
Yes  
Culture Type
Isolate  
Organism Type
Natural  
Uncultured Type
  
Commercial Strain
  
Commercial Strain Comments
  
ORGANISM TAXONOMY
NCBI Taxonomy ID 866789
NCBI Superkingdom
Bacteria  
NCBI Kingdom
  
NCBI Phylum
Proteobacteria  
NCBI Class
Gammaproteobacteria  
NCBI Order
Enterobacterales  
NCBI Family
Enterobacteriaceae  
NCBI Genus
Escherichia  
NCBI Species
Escherichia coli  
ISOLATION CLASSIFICATION
Ecosystem
Host-associated  
Ecosystem Category
Human  
Ecosystem Type
Excretory system  
Ecosystem Subtype
Urethra  
Specific Ecosystem
Urine  
ORGANISM EXTERNAL REFERENCES
Strain Info ID
Genbank 16S ID
GENERAL PROPERTIES
Oxygen Requirement
Facultative  
Cell Shape
Rod-shaped  
Motility
Motile  
Sporulation
Nonsporulating  
Temperature Range
Mesophile  
Salinity
  
pH
  
Cell Diameter
0.5um  
Cell Length
2um  
Color
Cream  
Gram Staining
Gram-  
Biotic Relationships Free living
Symbiotic Physical Interaction
  
Symbiotic Relationship
  
Symbiont Name
  
Symbiont Taxon ID
  
Cell Arrangements Singles
Pairs
Irregular colonies
Diseases Cystitis
Known Habitats Host
Human
Urogenital tract
Metabolisms
  
Phenotypes Pathogen
Energy Sources Heterotroph
CYANOBACTERIA METADATA
Filaments
  
Filament Type
  
Differentiated Cells
  
Position Of Heterocysts
  
Cysts
  
Mode Of Reproduction
  
Trichome
  
Trichome Type
  
Carotenoids
  
Pigments
  
Phage Infectivity
  
Phage Type
  
Restriction Enzyme
  
Toxin Production
  
Toxin Type
  
Secondary Metabolites
  
Developmental Cycle
  
Branching
  
Gas Vesicles
  
Gas Vesicle Type
  
Diagnostic Inclusion Body Information
  
Extracellular Structures
  
Bloom Forming
  
Pigment Type
  
Complementary chromatic adaptation (CCA)
  
Medium Types
  

 

 

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