Strain identifier

BacDive ID: 5216

Type strain: Yes

Species: Yersinia pseudotuberculosis

Strain Designation: 14

Strain history: CIP <- 1955, G. Girard, Inst. Pasteur, Paris, France, Yersinia rodentium <- E. Thal, Stockholm, Sweden: strain 14

NCBI tax ID(s): 1218101 (strain), 633 (species)

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General

@ref: 3456

BacDive-ID: 5216

DSM-Number: 8992

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

description: Yersinia pseudotuberculosis 14 is an aerobe, mesophilic, motile bacterium that was isolated from turkey.

NCBI tax id

NCBI tax idMatching level
1218101strain
633species

strain history

@refhistory
3456<- ATCC <- NCTC (Yersinia rodentium) <- E. Thal
67770R. Sakazaki 22176 <-- NCTC 10275 <-- E. Thal.
122003CIP <- 1955, G. Girard, Inst. Pasteur, Paris, France, Yersinia rodentium <- E. Thal, Stockholm, Sweden: strain 14

doi: 10.13145/bacdive5216.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Yersiniaceae
  • genus: Yersinia
  • species: Yersinia pseudotuberculosis
  • full scientific name: Yersinia pseudotuberculosis (Pfeiffer 1889) Smith and Thal 1965 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Bacillus pseudotuberkulosis
    20215Pasteurella lymphangitidis

@ref: 3456

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Yersiniaceae

genus: Yersinia

species: Yersinia pseudotuberculosis

full scientific name: Yersinia pseudotuberculosis (Pfeiffer 1889) Smith and Thal 1965

strain designation: 14

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.577
6948099.991negative
122003nonegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3456COLUMBIA BLOOD AGAR (DSMZ Medium 429)yeshttps://mediadive.dsmz.de/medium/429Name: COLUMBIA BLOOD AGAR (DSMZ Medium 429) Composition: Horse blood 40.0 g/l Columbia agar base
3456BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
38377MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122003CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
3456positivegrowth37mesophilic
38377positivegrowth30mesophilic
44861positivegrowth30-37mesophilic
67770positivegrowth37mesophilic
122003positivegrowth5-41

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
44861aerobe
122003facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.737

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
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
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68368L-arabinose-fermentation30849
68368amygdalin+fermentation27613
68368melibiose+fermentation28053
68368sucrose-fermentation17992
68368L-rhamnose-fermentation62345
68368sorbitol-fermentation30911
68368myo-inositol-fermentation17268
68368D-mannitol+fermentation16899
68368D-glucose+fermentation17634
68368gelatin-hydrolysis5291
68368tryptophan-energy source27897
68368urea+hydrolysis16199
68368citrate-assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
122003mannitol+fermentation29864
122003citrate-carbon source16947
122003glucose+fermentation17234
122003lactose-fermentation17716
122003nitrate+reduction17632
122003nitrite-reduction16301
122003malonate-assimilation15792
122003sodium thiosulfate-builds gas from132112
68377D-glucose+builds acid from17634
68377D-fructose+builds acid from15824
68377maltose-builds acid from17306
68377sucrose-builds acid from17992
68377ornithine-degradation18257
68377urea+hydrolysis16199
68377tryptophan-energy source27897

antibiotic resistance

  • @ref: 122003
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6837735581indoleno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12200335581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6837735581indole-
6836815688acetoin-
6836835581indole-
12200315688acetoin-
12200317234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase+3.2.1.21
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
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68377tryptophan deaminase-4.1.99.1
68377gamma-glutamyltransferase+2.3.2.2
68377proline-arylamidase+3.4.11.5
68377beta-galactosidase+3.2.1.23
68377alkaline phosphatase-3.1.3.1
68377lipase-
68377urease+3.5.1.5
68377ornithine decarboxylase-4.1.1.17
68377beta-lactamase-3.5.2.6
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23
122003oxidase-
122003beta-galactosidase+3.2.1.23
122003alcohol dehydrogenase-1.1.1.1
122003gelatinase-
122003catalase+1.11.1.6
122003lysine decarboxylase-4.1.1.18
122003ornithine decarboxylase-4.1.1.17
122003phenylalanine ammonia-lyase-4.3.1.24
122003tryptophan deaminase-
122003urease+3.5.1.5

fatty acid profile

  • @reffatty acidpercentageECL
    44861C12:01.812
    44861C14:01.214
    44861C16:035.416
    44861C17:00.517
    44861C12:0 ALDE ?2.410.915
    44861C14:0 3OH/C16:1 ISO I5.615.485
    44861C16:1 ω7c3215.819
    44861C17:0 CYCLO13.416.888
    44861C18:1 ω7c /12t/9t7.617.824
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG
  • @reffatty acidpercentageECL
    44861C12:02.812
    44861C14:01.614
    44861C15:00.915
    44861C16:028.716
    44861C17:00.717
    44861C18:00.618
    44861C14:0 3OH/C16:1 ISO I10.215.485
    44861C16:1 ω7c43.915.819
    44861C17:0 CYCLO5.516.888
    44861C18:1 ω7c /12t/9t5.117.824
  • 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
44861-++--+----++-+--+---
122003-+++-++-+-++-+-+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
3456+-----+----++----++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122003+/---++/-+-+/--++++-+--+---+-+++-+-+-+------------++/-+/--+/-

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
44861-++---+--+++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122003+++++-+--++---+--+++++-+--++---+++---+--+--------+------+--++--------------+---++-+---+--+-++-+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
3456turkeyStockholmSwedenSWEEurope
44861Turkey1952
67770Turkey
122003Animal, TurkeyStockholmSwedenSWEEurope

isolation source categories

  • Cat1: #Host
  • Cat2: #Birds

taxonmaps

  • @ref: 69479
  • File name: preview.99_140.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_106;97_113;98_124;99_140&stattab=map
  • Last taxonomy: Yersiniaceae
  • 16S sequence: KC776733
  • Sequence Identity:
  • Total samples: 33336
  • soil counts: 1734
  • aquatic counts: 5584
  • animal counts: 23907
  • plant counts: 2111

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
34562Risk group (German classification)
1220032Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Yersinia pseudotuberculosis 16S ribosomal RNA gene, partial sequenceAF3663751461ena633
20218Yersinia pseudotuberculosis strain ATCC 29833 16S ribosomal RNA gene, partial sequenceKC7767331450ena633
20218Yersinia pseudotuberculosis strain CCUG 5855 16S ribosomal RNA gene, partial sequenceFJ7173421460ena633
20218Yersinia pseudotuberculosis strain DSM 8992 16S ribosomal RNA gene, partial sequenceHM0075931356ena633

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Yersinia pseudotuberculosis NCTC10275GCA_900637475completencbi633
66792Yersinia pseudotuberculosis NBRC 1056921218101.3wgspatric1218101
66792Yersinia pseudotuberculosis strain NCTC10275633.147completepatric633
66792Yersinia pseudotuberculosis NBRC 1056922563367111draftimg1218101
66792Yersinia pseudotuberculosis NCTC102752844429765completeimg633
67770Yersinia pseudotuberculosis NBRC 105692GCA_000511675contigncbi1218101

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes60.244no
gram-positiveno98.531no
anaerobicno98.039yes
aerobicyes92.458no
halophileno90.84no
spore-formingno94.399no
thermophileno98.186yes
glucose-utilyes95.366no
motileyes91.602no
glucose-fermentyes94.625no

External links

@ref: 3456

culture collection no.: DSM 8992, ATCC 29833, CIP 55.85, NCTC 10275, CCUG 5855, JCM 1676, NBRC 105692

straininfo link

  • @ref: 74708
  • straininfo: 389426

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16832628Genomic comparison of Yersinia pestis and Yersinia pseudotuberculosis by combination of suppression subtractive hybridization and DNA microarray.Wang X, Zhou D, Qin L, Dai E, Zhang J, Han Y, Guo Z, Song Y, Du Z, Wang J, Wang J, Yang RArch Microbiol10.1007/s00203-006-0129-12006Cluster Analysis, DNA, Bacterial/*genetics, *Evolution, Molecular, *Genome, Bacterial, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Phylogeny, Synteny, Yersinia pestis/*genetics, Yersinia pseudotuberculosis/*geneticsGenetics
Metabolism30242257The Cytotoxic Necrotizing Factor of Yersinia pseudotuberculosis (CNFy) is Carried on Extracellular Membrane Vesicles to Host Cells.Monnappa AK, Bari W, Seo JK, Mitchell RJSci Rep10.1038/s41598-018-32530-y2018Bacterial Outer Membrane Proteins/*metabolism, Biological Transport/physiology, Cell Line, Tumor, Extracellular Vesicles/*metabolism, HeLa Cells, Humans, Virulence/physiology, Virulence Factors/*metabolism, Yersinia pseudotuberculosis/*pathogenicity, Yersinia pseudotuberculosis Infections/*metabolism/*microbiologyPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3456Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8992)https://www.dsmz.de/collection/catalogue/details/culture/DSM-8992
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
38377Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6683
44861Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 5855)https://www.ccug.se/strain?id=5855
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/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
68377Automatically annotated from API NH
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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
74708Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389426.1StrainInfo: A central database for resolving microbial strain identifiers
122003Curators of the CIPCollection of Institut Pasteur (CIP 55.85)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2055.85