Strain identifier

BacDive ID: 5227

Type strain: Yes

Species: Yersinia kristensenii

Strain history: CIP <- 1980, H.H. Mollaret, Inst. Pasteur, Paris, France: strain CNY 105

NCBI tax ID(s): 28152 (species)

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General

@ref: 7583

BacDive-ID: 5227

DSM-Number: 18543

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Yersinia kristensenii DSM 18543 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from urine.

NCBI tax id

  • NCBI tax id: 28152
  • Matching level: species

strain history

@refhistory
7583<- CIP <- H. H. Mollaret, Institut Pasteur, Paris
377171980, H.H. Mollaret, Inst. Pasteur, Paris, France: strain CNY 105
67770R. Sakazaki 476 <-- ATCC 33638 <-- D. J. Brenner CDC 1458-81 <-- H. Bercovier IP 105 <-- M. Kristensen MK104 <-- W. Frederiksen P226.
120501CIP <- 1980, H.H. Mollaret, Inst. Pasteur, Paris, France: strain CNY 105

doi: 10.13145/bacdive5227.20230509.8.1

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 kristensenii
  • full scientific name: Yersinia kristensenii Bercovier et al. 1981

@ref: 7583

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Yersiniaceae

genus: Yersinia

species: Yersinia kristensenii subsp. kristensenii

full scientific name: Yersinia kristensenii subsp. kristensenii Cunningham et al. 2019

type strain: yes

Morphology

cell morphology

  • @ref: 120501
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7583TRYPTICASE 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
37717MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
120501CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
120501CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7583positivegrowth30mesophilic
37717positivegrowth30mesophilic
67770positivegrowth26mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120501
  • oxygen tolerance: facultative anaerobe

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
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
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
120501nitrate+reduction17632
120501nitrite-reduction16301

metabolite production

  • @ref: 120501
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

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
120501oxidase-
120501catalase+1.11.1.6
120501urease+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
120501-+++-++-+-++-+-+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120501+--+++---+++++--+++--+-++/-+/-+++--+---+/---+----++-+-+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7583urineDenmarkDNKEurope
67770Human urine
120501Human, UrineDenmarkDNKEurope

isolation source categories

  • Cat1: #Host Body Product
  • Cat2: #Fluids
  • Cat3: #Urine

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
75832Risk group (German classification)
1205012Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Yersinia kristensenii strain ATCC 33638 16S ribosomal RNA gene, partial sequenceAY332832466ena28152
20218Yersinia kristensenii strain CCUG 11294 16S ribosomal RNA gene, partial sequenceEF1791261461ena28152
7583Yersinia kristensenii 16S ribosomal RNA gene, partial sequenceAF3663811461ena28152

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Yersinia kristensenii ATCC 33638527012.3wgspatric527012
66792Yersinia kristensenii strain NCTC1147128152.30wgspatric28152
66792Yersinia kristensenii ATCC 33638645058790draftimg527012
67770Yersinia kristensenii ATCC 33638GCA_000173715contigncbi527012
67770Yersinia kristensenii NCTC11471GCA_900460525contigncbi28152

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.887no
anaerobicno96.641no
halophileno93.826no
spore-formingno93.164no
glucose-utilyes94.48no
motileyes90.815no
thermophileno99.273yes
aerobicyes92.267no
flagellatedyes57.737no
glucose-fermentyes94.465no

External links

@ref: 7583

culture collection no.: DSM 18543, ATCC 33638, CCUG 11294, CIP 80.30, NCTC 11471, JCM 7576, CCUG 8241, CDC 1458-81, CNY 105

straininfo link

  • @ref: 74719
  • straininfo: 10839

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism28398546The CDI toxin of Yersinia kristensenii is a novel bacterial member of the RNase A superfamily.Batot G, Michalska K, Ekberg G, Irimpan EM, Joachimiak G, Jedrzejczak R, Babnigg G, Hayes CS, Joachimiak A, Goulding CWNucleic Acids Res10.1093/nar/gkx2302017Bacterial Toxins/*chemistry/metabolism, Crystallography, X-Ray, Endoribonucleases/*chemistry, Models, Molecular, Protein Conformation, RNA/metabolism, Ribonuclease, Pancreatic/*chemistry/metabolism, Yersinia/*enzymologyPathogenicity
Phylogeny31066656Yersinia hibernica sp. nov., isolated from pig-production environments.Nguyen SV, Muthappa DM, Hurley D, Donoghue O, McCabe E, Anes J, Schaffer K, Murphy BP, Buckley JF, Fanning SInt J Syst Evol Microbiol10.1099/ijsem.0.0034222019Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Ireland, Palatine Tonsil/microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Swine/*microbiology, Yersinia/*classification/isolation & purificationTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7583Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18543)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18543
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
37717Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11124
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
74719Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10839.1StrainInfo: A central database for resolving microbial strain identifiers
120501Curators of the CIPCollection of Institut Pasteur (CIP 80.30)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2080.30