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BacDive ID 138285
Type strain
Strain Designation RM45EM
Culture col. no. CIP 105993 RM45EM ECOR 69
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: 39420

BacDive-ID: 138285

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

description: Escherichia coli RM45EM 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: 39420
  • history: CIP <- 1999, T.S. Whittam, Pennsylvania Ste Univ., PA, USA: strain ECOR 69 <- H. Ochman and R.K. Selander: strain RM45EM

doi: 10.13145/bacdive138285.20251217.10

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: 39420

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacterales

family: Enterobacteriaceae

genus: Escherichia

species: Escherichia coli

strain designation: RM45EM

type strain: no

Morphology

cell morphology

  • @ref: 39420
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 39420

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
39420MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
39420CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
39420positivegrowth30
39420positivegrowth30-41
39420negativegrowth5
39420negativegrowth10

Physiology and metabolism

oxygen tolerance

  • @ref: 39420
  • oxygen tolerance: facultative anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3942029864mannitol+fermentation
3942016947citrate-carbon source
394204853esculin-hydrolysis
3942017234glucose+fermentation
3942017716lactose+fermentation
3942017632nitrate+reduction
3942016301nitrite+reduction
3942015792malonate-assimilation
39420132112sodium thiosulfate-builds gas from
3942017234glucose+degradation
6837128087glycogen-builds acid from
6837117151xylitol-builds acid from
6837132528turanose-builds acid from
6837128017starch-builds acid from
6837127613amygdalin-builds acid from
6837118305arbutin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837117924D-sorbitol+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837116899D-mannitol+builds acid from
6837112936D-galactose+builds acid from
68371Potassium 5-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol+builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose+builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose+builds acid from
6837162318D-lyxose-builds acid from
6837116634raffinose+builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose-builds acid from
6837159640N-acetylglucosamine+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
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
6837117108D-arabinose+builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from

antibiotic resistance

  • @ref: 39420
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 39420
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
3942015688acetoin-
3942017234glucose+

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
39420oxidase-
39420beta-galactosidase+3.2.1.23
39420alcohol dehydrogenase-1.1.1.1
39420gelatinase-
39420catalase+1.11.1.6
39420lysine decarboxylase+4.1.1.18
39420ornithine decarboxylase+4.1.1.17
39420phenylalanine ammonia-lyase-4.3.1.24
39420tryptophan deaminase-
39420urease-3.5.1.5
68382alpha-mannosidase-3.2.1.24

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
39420-+---+----++++------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
39420+-++++---+++++++-++--+--+/-+/--++++/-+--+---+/---+-+-+-+/--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
39420+++++++-+++++++-++++++-++----+++-+--+--+---++--+++----++---++----++-++--+--++--+++++----+++++++-+--

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrycontinentsample type
39420WashingtonUSAUSANorth America
39420WashingtonUnited States of AmericaUSANorth AmericaAnimal, Celebese ape, healthy

Interaction and safety

risk assessment

  • @ref: 39420
  • biosafety level: 2
  • biosafety level comment: Risk group (French classification)

Sequence information

Genome sequences

@refdescriptionassembly levelINSDC accessionNCBI tax IDscore
124043PDT000619955.1 assembly for Escherichia coli ECOR-69contigGCA_01253025556236.6
124043PDT000827792.1 assembly for Escherichia coli ECOR-69contigGCA_01446320556237.2

Literature

@ref: 39420

culture collection no.: CIP 105993, ECOR 69

straininfo link

  • @ref: 126262
  • straininfo: 68452

literature

Pubmed-IDtitleauthorsjournalDOIyearmeshtopictopic2
9055066Bacterial interspersed mosaic elements (BIMEs) are a major source of sequence polymorphism in Escherichia coli intergenic regions including specific associations with a new insertion sequence.Bachellier S, Clement JM, Hofnung M, Gilson E.Genetics10.1093/genetics/145.3.5511997genetics, genetics, Escherichia coli Proteins, DNA Transposable Elements, Mosaicism, Polymorphism, Genetic
10198021Accessory DNA in the genomes of representatives of the Escherichia coli reference collection.Hurtado A, Rodriguez-Valera F.J Bacteriol10.1128/jb.181.8.2548-2554.19991999genetics, genetics, Genes, Bacterial, Genome, Bacterial, Genetic VariationGenetics
14702297Osmoregulatory 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, analysisMetabolism
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
16751485Yersiniabactin production by Pseudomonas syringae and Escherichia coli, and description of a second yersiniabactin locus evolutionary group.Bultreys A, Gheysen I, de Hoffmann E.Appl Environ Microbiol10.1128/aem.00119-062006metabolism, metabolism, metabolism, metabolism, Evolution, MolecularMetabolism
35242119Combination Effect of Engineered Endolysin EC340 With Antibiotics.Hong HW, Kim YD, Jang J, Kim MS, Song M, Myung H.Front Microbiol10.3389/fmicb.2022.8219362022Bacteriophage, Colistin, synergy, Gram-negative Bacteria, Endolysin, Antibacterial Agent, Cecropin A
35495085Enterobacteria 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, Sv76PathogenicityGenetics
36199530Enterobacteria 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 GenomePathogenicityGenetics

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
39420Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105993Collection of Institut Pasteur (CIP 105993)
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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