Strain identifier

BacDive ID: 5217

Type strain: Yes

Species: Yersinia enterocolitica subsp. palearctica

Strain Designation: Y11

Strain history: CIP <- 2001, H. Neubauer, BSW Sanitätsakademie des Bundeswehr, München, Germany: strain Y11

NCBI tax ID(s): 150053 (subspecies)

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General

@ref: 4877

BacDive-ID: 5217

DSM-Number: 13030

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, antibiotic resistance

description: Yersinia enterocolitica subsp. palearctica Y11 is an aerobe, Gram-negative bacterium that has multiple antibiotic resistances and was isolated from human stool.

NCBI tax id

  • NCBI tax id: 150053
  • Matching level: subspecies

strain history

@refhistory
4877<- E. J. Finke; <- Inst. Microbiol. Sanitätsakad. der Bundeswehr; <- Zentrales Inst. des sanitätsdienstes der Bundeswehr; <- Hygiene Inst.;
418702001, H. Neubauer, BSW Sanitätsakademie des Bundeswehr, München, Germany, strain Y11
119060CIP <- 2001, H. Neubauer, BSW Sanitätsakademie des Bundeswehr, München, Germany: strain Y11

doi: 10.13145/bacdive5217.20240916.9.1

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 enterocolitica subsp. palearctica
  • full scientific name: Yersinia enterocolitica subsp. palearctica Neubauer et al. 2000

@ref: 4877

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Yersiniaceae

genus: Yersinia

species: Yersinia enterocolitica subsp. palearctica

full scientific name: Yersinia enterocolitica subsp. palearctica Neubauer et al. 2000

strain designation: Y11

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
119060negativerod-shapedyes
69480negative100

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4877COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
4877NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
41870MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
4877TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
119060CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
4877positivegrowth28
41870positivegrowth30
59691positivegrowth30
4877positivegrowth30
119060positivegrowth10-41
119060nogrowth5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59691aerobe
119060facultative anaerobe

antibiogram

  • @ref: 4877
  • medium: Mueller Hinton
  • incubation temperature: 30
  • oxygen condition: aerob
  • Penicillin G: 0
  • oxacillin: 0
  • ampicillin: 0
  • ticarcillin: 12
  • mezlocillin: 32
  • cefalotin: 6
  • cefazolin: 16
  • cefotaxime: 42
  • aztreonam: 38
  • imipenem: 34-36
  • tetracycline: 30
  • chloramphenicol: 28-30
  • gentamycin: 20
  • amikacin: 22
  • vancomycin: 0
  • erythromycin: 12
  • lincomycin: 0
  • ofloxacin: 30-32
  • norfloxacin: 30-32
  • colistin: 16
  • pipemidic acid: 26-28
  • nitrofurantoin: 20
  • bacitracin: 0
  • polymyxin b: 18
  • kanamycin: 22
  • neomycin: 18
  • doxycycline: 24-26
  • ceftriaxone: 30
  • clindamycin: 10
  • fosfomycin: 40
  • moxifloxacin: 30
  • linezolid: 10
  • nystatin: 0
  • quinupristin/dalfopristin: 10
  • teicoplanin: 0
  • piperacillin/tazobactam: 34-36

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 90.7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose+fermentation
6836827613amygdalin+fermentation
6836828053melibiose-fermentation
6836817992sucrose+fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol+fermentation
6836817268myo-inositol+fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine+degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
11906029864mannitol+fermentation
11906017234glucose+fermentation
11906017716lactose+fermentation
11906017632nitrate+reduction
11906016301nitrite-reduction
119060132112sodium thiosulfate-builds gas from
6837217754glycerol+assimilation
6837217113erythritol-assimilation
6837217108D-arabinose-assimilation
6837230849L-arabinose+assimilation
6837216988D-ribose+assimilation
6837265327D-xylose-assimilation
6837265328L-xylose-assimilation
6837215963ribitol-assimilation
6837274863methyl beta-D-xylopyranoside-assimilation
6837212936D-galactose+assimilation
6837217634D-glucose+assimilation
6837215824D-fructose+assimilation
6837216024D-mannose+assimilation
6837217266L-sorbose+assimilation
6837262345L-rhamnose-assimilation
6837216813galactitol+assimilation
6837217268myo-inositol+assimilation
6837216899D-mannitol+assimilation
6837230911sorbitol+assimilation
6837243943methyl alpha-D-mannoside-assimilation
68372320061methyl alpha-D-glucopyranoside-assimilation
6837259640N-acetylglucosamine+assimilation
6837227613amygdalin-assimilation
6837218305arbutin+assimilation
683724853esculin-assimilation
6837217814salicin-assimilation
6837217057cellobiose+assimilation
6837217306maltose+assimilation
6837217716lactose-assimilation
6837228053melibiose-assimilation
6837217992sucrose+assimilation
6837227082trehalose+assimilation
6837215443inulin-assimilation
683726731melezitose-assimilation
6837216634raffinose-assimilation
6837228017starch-assimilation
6837228087glycogen-assimilation
6837217151xylitol-assimilation
6837228066gentiobiose+assimilation
6837232528turanose-assimilation
6837262318D-lyxose-assimilation
6837216443D-tagatose-assimilation
6837228847D-fucose-assimilation
6837218287L-fucose-assimilation
6837218333D-arabitol-assimilation
6837218403L-arabitol-assimilation
6837224265gluconate+assimilation
68372Potassium 2-ketogluconate-assimilation
68372Potassium 5-ketogluconate+assimilation

metabolite production

@refChebi-IDmetaboliteproduction
6836835581indoleno
6836816136hydrogen sulfideno
11906035581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836835581indole-
11906015688acetoin-
11906017234glucose+

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
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
119060oxidase-
119060beta-galactosidase+3.2.1.23
119060alcohol dehydrogenase-1.1.1.1
119060gelatinase-
119060catalase+1.11.1.6
119060lysine decarboxylase-4.1.1.18
119060ornithine decarboxylase+4.1.1.17
119060tryptophan deaminase-
119060urease+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
119060-+++++++--++++-+-+--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
4877+--+--+----++++-+-++-
4877+--+--+--+-++++-+-++-

API 50CHas

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
4877-+--++----+++++-++++--+-+--++--++------+-------+-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119060++++++-+-++--+-+-+-++----------+++--+------------+----++++-++------------------++--------++-+++----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
4877human stoolHamburgGermanyDEUEurope53.575310.0153
59691Human stoolGermanyDEUEurope
119060Human, FecesMünchenGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Gastrointestinal tract#Feces (Stool)
#Host#Human

taxonmaps

  • @ref: 69479
  • File name: preview.99_144.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_106;97_113;98_125;99_144&stattab=map
  • Last taxonomy: Yersiniaceae
  • 16S sequence: U63135
  • Sequence Identity:
  • Total samples: 5799
  • soil counts: 402
  • aquatic counts: 1559
  • animal counts: 3499
  • plant counts: 339

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
48772Risk group (German classification)
1190602Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Yersinia enterocolitica subsp. palearctica strain DSM 13030 16S ribosomal RNA gene, partial sequenceFJ7173441484nuccore150053
4877Yersinia enterocolitica 16S ribosomal RNA gene, partial sequenceU631351367nuccore630

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Yersinia enterocolitica subsp. palearctica Y11GCA_000253175completencbi930944
66792Yersinia enterocolitica subsp. palearctica Y11930944.6completepatric930944
66792Yersinia enterocolitica subsp. palearctica Y11930944.24plasmidpatric930944

GC content

  • @ref: 4877
  • GC-content: 44.2

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno100no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.454yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no65.472no
69480spore-formingspore-formingAbility to form endo- or exosporesno90.7no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno99.5no
69480flagellatedmotile2+Ability to perform flagellated movementyes78.415no

External links

@ref: 4877

culture collection no.: DSM 13030, CCUG 52867, CECT 9144, CIP 106945, WDCM 00216

straininfo link

  • @ref: 74709
  • straininfo: 49390

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4877Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13030)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13030
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
41870Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19131
59691Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52867)https://www.ccug.se/strain?id=52867
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)
68368Automatically annotated from API 20E
68372Automatically annotated from API 50CH assim
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)
74709Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49390.1StrainInfo: A central database for resolving microbial strain identifiers
119060Curators of the CIPCollection of Institut Pasteur (CIP 106945)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106945