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BacDive ID 138282
Type strain
Strain Designation RM183E
Culture col. no. CIP 105989 ECOR 23 RM183E
NCBI tax ID(s) 562
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 10 (current version):
version 10 (current version)

General

@ref: 39417

BacDive-ID: 138282

keywords: genome sequence, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Escherichia coli RM183E is a facultative anaerobe, mesophilic, Gram-negative prokaryote of the family Enterobacteriaceae.

NCBI tax id

  • NCBI tax id: 562
  • Matching level: species

strain history

  • @ref: 39417
  • history: CIP <- 1999, T.S. Whittam, Pennsylvania Ste Univ., PA, USA: strain ECOR 23 <- H. Ochman and R.K. Selander: strain RM183E

doi: 10.13145/bacdive138282.20251217.10

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: kingdom/pseudomonadati
  • keyword: phylum/pseudomonadota
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Escherichia
  • species: Escherichia coli
  • full scientific name: Escherichia coli (Migula 1895) Castellani and Chalmers 1919 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Bacillus coli

@ref: 39417

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacterales

family: Enterobacteriaceae

genus: Escherichia

species: Escherichia coli

strain designation: RM183E

type strain: no

Morphology

cell morphology

  • @ref: 39417
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 39417

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
39417MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
39417CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
39417positivegrowth30
39417positivegrowth30-41
39417negativegrowth5
39417negativegrowth10

Physiology and metabolism

oxygen tolerance

  • @ref: 39417
  • oxygen tolerance: facultative anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3941729864mannitol+fermentation
3941716947citrate-carbon source
394174853esculin+hydrolysis
3941717234glucose+fermentation
3941717716lactose+fermentation
3941717632nitrate+reduction
3941716301nitrite+reduction
3941715792malonate-assimilation
39417132112sodium thiosulfate-builds gas from
3941717234glucose+degradation
68371Potassium 2-ketogluconate-builds acid from
6837118287L-fucose+builds acid from
6837118333D-arabitol-builds acid from
6837118403L-arabitol-builds acid from
6837128847D-fucose-builds acid from
6837117992sucrose-builds acid from
6837127082trehalose+builds acid from
6837117716lactose+builds acid from
6837117057cellobiose-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837117754glycerol+builds acid from
68371Potassium 5-ketogluconate+builds acid from
6837124265gluconate+builds acid from
6837116443D-tagatose+builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837117151xylitol-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837117306maltose+builds acid from
6837159640N-acetylglucosamine+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol+builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose+builds acid from
6837117266L-sorbose+builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117113erythritol-builds acid from

antibiotic resistance

  • @ref: 39417
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 39417
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
3941715688acetoin-
3941717234glucose+

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382esterase lipase (C 8)-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
39417oxidase-
39417beta-galactosidase+3.2.1.23
39417alcohol dehydrogenase-1.1.1.1
39417gelatinase-
39417catalase+1.11.1.6
39417lysine decarboxylase+4.1.1.18
39417ornithine decarboxylase+4.1.1.17
39417phenylalanine ammonia-lyase-4.3.1.24
39417tryptophan deaminase-
39417urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
39417-++--+----++-+-+-+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
39417+-+/-+++---++++++--++--+-+/-+/-+/--+++/--+----+/--+/---+-+--+-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
39417+++++++--++++++-++++++-++-----++-+--+--+---++----+----++-+-++--------------+---++-+---+--++++++-+-+

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample type
39417WashingtonUSAUSANorth America
39417WashingtonUnited States of AmericaUSANorth AmericaElephant, healthy

Interaction and safety

risk assessment

  • @ref: 39417
  • biosafety level: 2
  • biosafety level comment: Risk group (French classification)

Sequence information

Genome sequences

  • @ref: 124043
  • description: PDT000619905.1 assembly for Escherichia coli ECOR-23
  • assembly level: contig
  • INSDC accession: GCA_012531595
  • NCBI tax ID: 562
  • score: 20

Literature

@ref: 39417

culture collection no.: CIP 105989, ECOR 23

straininfo link

  • @ref: 126262
  • straininfo: 68514

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny1699928Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli.Herzer PJ, Inouye S, Inouye M, Whittam TS.J Bacteriol10.1128/jb.172.11.6175-6181.19901990genetics, genetics, genetics, Phylogeny
2050640Nucleotide sequences of the gnd genes from nine natural isolates of Escherichia coli: evidence of intragenic recombination as a contributing factor in the evolution of the polymorphic gnd locus.Bisercic M, Feutrier JY, Reeves PR.J Bacteriol10.1128/jb.173.12.3894-3900.19911991genetics, genetics, Recombination, Genetic, Polymorphism, Genetic, Genes, Bacterial
8253675The ancestry of insertion sequences common to Escherichia coli and Salmonella typhimurium.Bisercic M, Ochman H.J Bacteriol10.1128/jb.175.24.7863-7868.19931993genetics, genetics, DNA Transposable Elements, Biological Evolution
8384142Natural populations of Escherichia coli and Salmonella typhimurium harbor the same classes of insertion sequences.Bisercic M, Ochman H.Genetics10.1093/genetics/133.3.4491993genetics, genetics, DNA Transposable Elements
8536964Correlation of Rhs elements with Escherichia coli population structure.Hill CW, Feulner G, Brody MS, Zhao S, Sadosky AB, Sandt CH.Genetics10.1093/genetics/141.1.151995genetics, Genes, Bacterial
Phylogeny11010916Rapid and simple determination of the Escherichia coli phylogenetic group.Clermont O, Bonacorsi S, Bingen E.Appl Environ Microbiol10.1128/aem.66.10.4555-4558.20002000classification, genetics, Phylogeny
11500406Ongoing horizontal and vertical transmission of virulence genes and papA alleles among Escherichia coli blood isolates from patients with diverse-source bacteremia.Johnson JR, O'Bryan TT, Kuskowski M, Maslow JN.Infect Immun10.1128/iai.69.9.5363-5374.20012001genetics, pathogenicity, microbiology, microbiology, genetics, Escherichia coli Proteins, Gene Transfer, Horizontal
Metabolism14702297Osmoregulatory systems of Escherichia coli: identification of betaine-carnitine-choline transporter family member BetU and distributions of betU and trkG among pathogenic and nonpathogenic isolates.Ly A, Henderson J, Lu A, Culham DE, Wood JM.J Bacteriol10.1128/jb.186.2.296-306.20042004metabolism, metabolism, metabolism, metabolism, analysis, analysis
15150243The ETT2 gene cluster, encoding a second type III secretion system from Escherichia coli, is present in the majority of strains but has undergone widespread mutational attrition.Ren CP, Chaudhuri RR, Fivian A, Bailey CM, Antonio M, Barnes WM, Pallen MJ.J Bacteriol10.1128/jb.186.11.3547-3560.20042004genetics, genetics, Mutation, physiology, Multigene Family
17050815Phylogenetic comparisons reveal multiple acquisitions of the toxin genes by enterotoxigenic Escherichia coli strains of different evolutionary lineages.Turner SM, Chaudhuri RR, Jiang ZD, DuPont H, Gyles C, Penn CW, Pallen MJ, Henderson IR.J Clin Microbiol10.1128/jcm.01474-062006genetics, pathogenicity, genetics, genetics, Evolution, Molecular
30533715Draft Genome Sequences of the Escherichia coli Reference (ECOR) Collection.Patel IR, Gangiredla J, Mammel MK, Lampel KA, Elkins CA, Lacher DW.Microbiol Resour Announc10.1128/mra.01133-182018
Pathogenicity35495085Enterobacteria Phage SV76 Host Range and Genomic Characterization.Carmody CM, Farquharson EL, Nugen SR.Phage (New Rochelle)10.1089/phage.2022.00052022Host range, Bacteriophage, Whole Genome Sequencing, T2, Ecor, Sv76Genetics
Pathogenicity36199530Enterobacteria Phage Ac3's Genome Annotation and Host Range Analysis Against the ECOR Reference Library.Farquharson EL, Nugen SR.Phage (New Rochelle)10.1089/phage.2022.00082022Host range, Ac3, Ecor, Phage GenomeGenetics
Metabolism37724859The distinct transcriptome of virulence-associated phylogenetic group B2 Escherichia coli.Hogins J, Xuan Z, Zimmern PE, Reitzer L.Microbiol Spectr10.1128/spectrum.02085-232023Metabolism, Transcriptional regulation, Phylogenetic analysis, Transcription factors, Urinary tract infection, Escherichia Coli, pathogens

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
39417Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105989Collection of Institut Pasteur (CIP 105989)
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
126262A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. ReimerStrainInfo—the central database for linked microbial strain identifiers10.1093/database/baaf059

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