Studies
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56,335 |
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Biosamples
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196,988 |
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Sequencing Projects
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525,361 |
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Analysis Projects
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384,993 |
| Organisms | 484,222 |
| PROJECT INFORMATION | |
|---|---|
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GOLD Project ID
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Gp0007996
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Project Name
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Escherichia coli O1:K1:H7 U5/41, DSM 30083
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Other Names
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Legacy ER Project ID
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17781
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Legacy GOLD ID
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Gi07590
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| NCBI BioProject Name | Escherichia coli DSM 30083 = JCM 1649 = ATCC 11775 |
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NCBI BioProject Accession
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PRJNA50621 |
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NCBI Locus Tag
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Escco
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NCBI BioSample Accession
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SAMN00718807 |
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Source Sample ID
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|
| PI | Hans-Peter Klenk |
| Added By | Ionna Pagani on 2010-09-02 |
| Last Modified By | Hema Katta on 2018-12-20 |
| Project Comments |
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Project Status
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Permanent Draft
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Project Relevance
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Poultry Pathogen Bioenergy Comparative analysis Biotechnological GEBA |
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Sequencing Center
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DOE Joint Genome Institute (JGI)
(USA)
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Collaborating Institute
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Leibniz Institute
(Germany)
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Funding Agency
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U.S. Department of Energy (DOE)
(USA)
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Project Description
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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.
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| Is JGI Project |
Yes
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Project Information Visibility
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Public |
| PROJECT TYPE | |
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Specimen
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Organism |
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Nucleic Acid
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DNA |
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Sequencing Strategy
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Whole Genome Sequencing
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| EXTERNAL PROJECT LINKS | |
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JGI Data Utilization Status
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JGI Award DOI
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| JGI Portal Download | Raw Sequence Data |
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Genome Publications
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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. PubMed: 25780495 DOI: 10.1186/1944-3277-9-2 Nature biotechnology: 35(7):676-683 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. PubMed: 28604660 DOI: 10.1038/nbt.3886 |
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Other Publications
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Ignored Publications
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Unassigned Publications
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| SRA Experiment |
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| 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 (AP) |
1 |
| Number of Derived Analyis Projects (DAP) |
0
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| SEQUENCING INFORMATION | |
|---|---|
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Sequencing Status
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Complete |
| Sequencing Quality (MIGS-31) |
Level 3: Improved-High-Quality Draft |
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Finishing Goal
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Contamination Screening Input
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DNA Amplification Method
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Single Cell Lysis Protocol
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Single Cell Lysis Approach
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Sequencing Comments
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DNA Amplification Kit
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Sequencing Technology
(MIGS-29)
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Illumina GAIIx 454 GS FLX Titanium |
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Library Method
(MIGS-28)
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Library Layout
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Library Screening Method
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Number Of Reads
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Read Size
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5038133
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Vector
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| GC Percent |
51
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| Chromosome Count |
1
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| Plasmid Count |
1
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| ORGANISM NAME | |
|---|---|
| GOLD Organism ID |
Go0007996 |
| Organism Name |
Escherichia coli O1:K1:H7 U5/41, DSM 30083
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| Other names (alias, synonyms, short names, common names) |
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| Organism Domain |
BACTERIAL
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| Phylogeny |
PROTEOBACTERIA-GAMMA
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| Genus |
Escherichia
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| Genus Synonyms |
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| Species |
Escherichia coli
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| Subspecies |
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| Species Synonyms |
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| Strain |
U5/41
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| Strain Synonyms |
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| Serovar/Cultivar |
O1:K1:H7
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| Culture Collection ID |
DSM 30083
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| Type Strain |
Yes
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| Exemplar DOI |
10.1601/ex.3093
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| Exemplar Name |
Escherichia coli
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| Taxon DOI |
10.1601/tx.3093
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| Biosafety Level |
2
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| Organism Comments |
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| Cultured |
Yes
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| Culture Type |
Isolate
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| Organism Type |
Natural
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| Uncultured Type |
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| Commercial Strain |
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| Commercial Strain Comments |
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ORGANISM TAXONOMY
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| NCBI Taxonomy ID |
866789 |
| NCBI Superkingdom |
Bacteria
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| NCBI Kingdom |
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| NCBI Phylum |
Pseudomonadota
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| NCBI Class |
Gammaproteobacteria
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| NCBI Order |
Enterobacterales
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| NCBI Family |
Enterobacteriaceae
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| NCBI Genus |
Escherichia
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| NCBI Species |
Escherichia coli
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| ISOLATION CLASSIFICATION | |
| Ecosystem |
Host-associated
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| Ecosystem Category |
Mammals: Human
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| Ecosystem Type |
Urinary system
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| Ecosystem Subtype |
Urine
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| Specific Ecosystem |
Unclassified
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| ORGANISM EXTERNAL REFERENCES | |
| Strain Info ID |
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| Genbank 16S ID |
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| GENERAL PROPERTIES | |
|---|---|
| Oxygen Requirement |
Facultative
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| Cell Shape |
Rod-shaped
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| Motility |
Motile
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| Sporulation |
Nonsporulating
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| Temperature Range |
Mesophile
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| Salinity |
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| pH |
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| Cell Diameter |
0.5um
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| Cell Length |
2um
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| Color |
Cream
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| Gram Staining |
Gram-
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| Biotic Relationships | Free living |
| Symbiotic Physical Interaction |
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| Symbiotic Relationship |
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| Symbiont Name |
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| Symbiont Taxon ID |
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| Cell Arrangements |
Singles Pairs Irregular colonies |
| Diseases |
Cystitis |
| Known Habitats |
Host Human Urogenital tract |
| Metabolisms |
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| Phenotypes |
Pathogen |
| Energy Sources |
Heterotroph |
| CYANOBACTERIA METADATA | |
| Filaments |
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| Filament Type |
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| Differentiated Cells |
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| Position Of Heterocysts |
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| Cysts |
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| Mode Of Reproduction |
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| Trichome |
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| Trichome Type |
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| Carotenoids |
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| Pigments |
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| Phage Infectivity |
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| Phage Type |
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| Restriction Enzyme |
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| Toxin Production |
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| Toxin Type |
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| Secondary Metabolites |
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| Developmental Cycle |
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| Branching |
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| Gas Vesicles |
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| Gas Vesicle Type |
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| Diagnostic Inclusion Body Information |
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| Extracellular Structures |
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| Bloom Forming |
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| Pigment Type |
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| Complementary chromatic adaptation (CCA) |
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| Medium Types |
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