Strain identifier

BacDive ID: 4928

Type strain: Yes

Species: Pseudescherichia vulneris

Strain Designation: 875-72, 580

Strain history: CIP <- 1988, ATCC <- CDC: strain 875-72 <- Nat. Inst. Hlth., Bethesda, CA, USA: strain 580

NCBI tax ID(s): 1115515 (strain), 566 (species)

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General

@ref: 1772

BacDive-ID: 4928

DSM-Number: 4564

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile

description: Pseudescherichia vulneris 875-72 is an aerobe, mesophilic, motile bacterium that was isolated from human wound.

NCBI tax id

NCBI tax idMatching level
1115515strain
566species

strain history

@refhistory
1772<- ATCC; ATCC 33821 <- CDC, Atlanta; CDC 875-72 <- NIH; NIH 580
67770Y. Kosako 82084 <-- R. Sakazaki 501 <-- D. J. Brenner CDC 875-72 <-- NIH 580.
123895CIP <- 1988, ATCC <- CDC: strain 875-72 <- Nat. Inst. Hlth., Bethesda, CA, USA: strain 580

doi: 10.13145/bacdive4928.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Pseudescherichia
  • species: Pseudescherichia vulneris
  • full scientific name: Pseudescherichia vulneris (Brenner et al. 1983) Alnajar and Gupta 2017

  • synonyms

    • @ref: 20215
    • synonym: Escherichia vulneris

@ref: 1772

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Pseudescherichia

species: Pseudescherichia vulneris

full scientific name: Pseudescherichia vulneris (Brenner et al. 1983) Alnajar and Gupta 2017

strain designation: 875-72, 580

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes94.45
6948099.868negative
123895yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
40554MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
1772TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium92.pdf
1772COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium693.pdf
123895CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
123895CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
1772positivegrowth37mesophilic
40554positivegrowth30mesophilic
46328positivegrowth30-37mesophilic
67770positivegrowth37mesophilic
123895positivegrowth30-41
123895nogrowth5psychrophilic
123895nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
46328aerobe
123895facultative anaerobe

spore formation

@refspore formationconfidence
69481no97
69480no99.725

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate+builds acid from
68371gluconate+builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose+builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose+builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose+builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
123895mannitol+fermentation29864
123895citrate-carbon source16947
123895nitrate+reduction17632
123895nitrite-reduction16301
123895malonate+assimilation15792
123895sodium thiosulfate-builds gas from132112

antibiotic resistance

  • @ref: 123895
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 123895
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12389515688acetoin-
12389517234glucose+

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
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
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
123895oxidase-
123895beta-galactosidase+3.2.1.23
123895alcohol dehydrogenase-1.1.1.1
123895gelatinase-
123895catalase+1.11.1.6
123895lysine decarboxylase+4.1.1.18
123895ornithine decarboxylase-4.1.1.17
123895tryptophan deaminase-
123895urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    46328C14:02.414
    46328C16:034.116
    46328C18:00.818
    46328C11:0 ISO 3OH712.09
    46328C14:0 3OH/C16:1 ISO I1015.485
    46328C16:1 ω7c1715.819
    46328C17:0 CYCLO7.116.888
    46328C18:1 ω7c /12t/9t18.417.824
    46328C19:0 ISO0.918.633
    46328unknown 13.961113.961
    46328unknown 14.5031.314.503
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123895-+---+----++++--+---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123895+--+++---++++-+--+---+-+++++++++--+---+-+-----++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
1772human wound
46328Human woundBethesdaUSAUSANorth America
67770Human woundBethesda, MDUSAUSANorth America
123895Human, Wound

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Other#Wound

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
17722Risk group (German classification)
1238951Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Escherichia vulneris strain ATCC 33821 16S ribosomal RNA gene, partial sequenceAF5304761468ena566
20218E.vulneris (ATCC 33821T) gene for 16S rRNAX807341443ena566
20218Escherichia vulneris gene for 16S rRNA, partial sequence, strain: NBRC 102420AB6817761465ena566

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Escherichia vulneris NBRC 1024201115515.3wgspatric1115515
66792Pseudescherichia vulneris strain NCTC12130566.6wgspatric566
66792Pseudescherichia vulneris NBRC 1024202600255014draftimg1115515
66792Pseudescherichia vulneris NCTC 121302806310681draftimg566
67770Pseudescherichia vulneris NBRC 102420GCA_000759795contigncbi1115515
67770Pseudescherichia vulneris NCTC12130GCA_900450975contigncbi566

GC content

  • @ref: 67770
  • GC-content: 58.5-58.7
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno97no
motileyes89.362no
flagellatedno72.923no
gram-positiveno97.976no
anaerobicno97.271no
aerobicyes69.259no
halophileno80.775no
spore-formingno94.809no
glucose-utilyes95.052no
thermophileno99.315yes
glucose-fermentyes90.83no

External links

@ref: 1772

culture collection no.: CCUG 15715, DSM 4564, ATCC 33821, IAM 14239, JCM 1688, NIH 580, CDC 875-72, BCRC 15953, CGMCC 1.3441, CIP 103177, HAMBI 1694, LMG 7868, NBRC 102420, NCTC 12130

straininfo link

  • @ref: 74425
  • straininfo: 2808

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny7107843Escherichia vulneris: a new species of Enterobacteriaceae associated with human wounds.Brenner DJ, McWhorter AC, Knutson JK, Steigerwalt AGJ Clin Microbiol10.1128/jcm.15.6.1133-1140.19821982Anti-Bacterial Agents/pharmacology, Base Composition, DNA, Bacterial/analysis, Enterobacteriaceae Infections/*microbiology, Escherichia/*classification/isolation & purification/physiology, Humans, Nucleic Acid Hybridization, Terminology as Topic, Wound Infection/*microbiologyPathogenicity
Phylogeny25851592Escherichia marmotae sp. nov., isolated from faeces of Marmota himalayana.Liu S, Jin D, Lan R, Wang Y, Meng Q, Dai H, Lu S, Hu S, Xu JInt J Syst Evol Microbiol10.1099/ijs.0.0002282015Animals, Base Composition, China, DNA, Bacterial/genetics, Escherichia/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Feces/*microbiology, Marmota/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1772Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4564)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4564
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
40554Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14946
46328Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 15715)https://www.ccug.se/strain?id=15715
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
74425Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2808.1StrainInfo: A central database for resolving microbial strain identifiers
123895Curators of the CIPCollection of Institut Pasteur (CIP 103177)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103177