Strain identifier

BacDive ID: 5230

Type strain: Yes

Species: Yersinia nurmii

Strain Designation: APN3a-c

Strain history: CIP <- 2010, DSMZ <- A. Murros-Kontiainen, Helsinki Univ., Helsinki, Finland: strain APN3a-c

NCBI tax ID(s): 685706 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 16251

BacDive-ID: 5230

DSM-Number: 22296

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

description: Yersinia nurmii APN3a-c is an aerobe, mesophilic, motile bacterium that was isolated from broiler meat packaged under a modified atmosphere.

NCBI tax id

  • NCBI tax id: 685706
  • Matching level: species

strain history

@refhistory
16251<- A. Murros-Kontiainen, Faculty Veterinary Medicine, Univ. Helsinki, Finland; APN3a-c
121373CIP <- 2010, DSMZ <- A. Murros-Kontiainen, Helsinki Univ., Helsinki, Finland: strain APN3a-c

doi: 10.13145/bacdive5230.20230509.8.1

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 nurmii
  • full scientific name: Yersinia nurmii Murros-Kontiainen et al. 2011

@ref: 16251

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Yersiniaceae

genus: Yersinia

species: Yersinia nurmii

full scientific name: Yersinia nurmii Murros-Kontiainen et al. 2011

strain designation: APN3a-c

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.907
6948099.966negative
121373nonegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16251TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
37586MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121373CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
16251positivegrowth28mesophilic
37586positivegrowth30mesophilic
62484positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
62484aerobe
121373facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.087

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
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
68371maltose+builds acid from17306
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
121373nitrate+reduction17632
121373nitrite-reduction16301

metabolite production

  • @ref: 121373
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
121373oxidase-
121373catalase+1.11.1.6
121373urease-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
121373-+++-+--+-++-+-+-+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121373+---+----++++----+---+----+/-++/--++--------------+/---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
16251broiler meat packaged under a modified atmosphereHelsinkiFinlandFINEurope
62484Packed broiler meat cutsFinlandFINEurope2005
121373Food, Broiler meat packaged under modified atmosphereHelsinkiFinlandFINEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Bottled, canned, packed food
#Engineered#Food production#Meat
#Host#Birds#Chicken

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
162511Risk group (German classification)
1213732Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16251
  • description: Yersinia nurmii strain APN3a-c 16S ribosomal RNA gene, partial sequence
  • accession: FJ717338
  • length: 1484
  • database: ena
  • NCBI tax ID: 685706

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Yersinia nurmii CIP110231TGCA_001112925scaffoldncbi685706
66792Yersinia nurmii CIP1102312667528026draftimg685706

GC content

  • @ref: 16251
  • GC-content: 48.7
  • method: fluorimetric

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.244no
flagellatedno56.385no
gram-positiveno98.514no
anaerobicno98.296no
aerobicyes90.765yes
halophileno92.331no
spore-formingno95.179no
glucose-utilyes94.238no
thermophileno98.189yes
glucose-fermentyes93.687no

External links

@ref: 16251

culture collection no.: CCUG 60891, DSM 22296, CIP 110231, LMG 25213

straininfo link

  • @ref: 74722
  • straininfo: 378361

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21037032Yersinia nurmii sp. nov.Murros-Kontiainen A, Fredriksson-Ahomaa M, Korkeala H, Johansson P, Rahkila R, Bjorkroth JInt J Syst Evol Microbiol10.1099/ijs.0.024836-02010Animals, Bacterial Proteins/genetics, Bacterial Typing Techniques, Chickens, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Meat/*microbiology, Molecular Sequence Data, Multilocus Sequence Typing, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Yersinia/*classification/genetics/*isolation & purificationGenetics
Genetics27187466The Draft Genome Sequence of the Yersinia entomophaga Entomopathogenic Type Strain MH96T.Hurst MR, Beattie A, Altermann E, Moraga RM, Harper LA, Calder J, Laugraud AToxins (Basel)10.3390/toxins80501432016Bacterial Proteins/genetics, Computational Biology, Computer Simulation, DNA, Bacterial/analysis, *Genome, Bacterial, Virulence/genetics, Yersinia/*genetics

Reference

@idauthorscataloguedoi/urltitle
16251Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22296)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22296
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
37586Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8067
62484Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 60891)https://www.ccug.se/strain?id=60891
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)
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
74722Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID378361.1StrainInfo: A central database for resolving microbial strain identifiers
121373Curators of the CIPCollection of Institut Pasteur (CIP 110231)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110231