Strain identifier

BacDive ID: 5224

Type strain: Yes

Species: Yersinia intermedia

Strain history: CIP <- 1980, H.H. Mollaret, Inst. Pasteur, Paris, France: strain CNY 3953

NCBI tax ID(s): 349965 (strain), 631 (species)

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General

@ref: 7570

BacDive-ID: 5224

DSM-Number: 18517

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

description: Yersinia intermedia DSM 18517 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from urine.

NCBI tax id

NCBI tax idMatching level
349965strain
631species

strain history

@refhistory
7570<- CIP <- H. H. Mollaret, Insitut Pasteur, Paris
418721980, H.H. Mollaret, Inst. Pasteur, Paris, France: strain CNY 3953
67770R. Sakazaki 456 <-- D. J. Brenner <-- B. Chester 48.
120148CIP <- 1980, H.H. Mollaret, Inst. Pasteur, Paris, France: strain CNY 3953

doi: 10.13145/bacdive5224.20230509.8.1

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 intermedia
  • full scientific name: Yersinia intermedia Brenner et al. 1981

@ref: 7570

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Yersiniaceae

genus: Yersinia

species: Yersinia intermedia

full scientific name: Yersinia intermedia Brenner et al. 1981

type strain: yes

Morphology

cell morphology

  • @ref: 120148
  • gram stain: negative
  • cell shape: rod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7570TRYPTICASE 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
7570COLUMBIA 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
41872MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
120148CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
120148CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
7570positivegrowth30mesophilic
41872positivegrowth30mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

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

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleyes
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole+

enzymes

@refvalueactivityec
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

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    45418C12:06.812
    45418C13:00.813
    45418C14:01.314
    45418C15:0515
    45418C16:023.716
    45418C17:02.617
    45418C12:0 ALDE ?2.510.915
    45418C14:0 3OH/C16:1 ISO I5.115.485
    45418C16:1 ω7c3315.819
    45418C17:0 CYCLO1016.888
    45418C18:1 ω7c /12t/9t9.417.824
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
7570+--++-+-++-+++++++++-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7570urineFranceFRAEurope
45418Human urine
67770Human urine
120148Human, UrineFranceFRAEurope

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
75702Risk group (German classification)
1201482Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Yersinia intermedia 16S ribosomal RNA gene, partial sequenceAF3663801461ena349965
20218Yersinia intermedia strain ATCC 29909 16S ribosomal RNA gene, partial sequence; and 16S-23S ribosomal RNA intergenic spacer, complete sequenceDQ095211807ena349965
20218Yersinia intermedia strain CCUG 11292 16S ribosomal RNA gene, partial sequenceEF1791231461ena631
7570Yersinia intermedia strain ATCC 29909 16S ribosomal RNA gene, partial sequenceAY332825388ena349965
67770Yersinia intermedia JCM 7579 gene for 16S ribosomal RNA, partial sequenceLC5040421465ena631

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Yersinia intermedia NCTC11469GCA_900635455completencbi631
66792Yersinia intermedia ATCC 29909349965.6wgspatric349965
66792Yersinia intermedia strain NCTC11469631.33completepatric631
66792Yersinia intermedia ATCC 29909638341240draftimg349965
67770Yersinia intermedia ATCC 29909GCA_000168035contigncbi349965

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes54.746no
gram-positiveno98.469no
anaerobicno95.991no
aerobicyes87.249no
halophileno93.383no
spore-formingno92.65no
thermophileno99.235no
glucose-utilyes96.045no
motileyes90.92no
glucose-fermentyes93.845yes

External links

@ref: 7570

culture collection no.: DSM 18517, ATCC 29909, CCUG 11292, CECT 4317, CIP 80.28, NCTC 11469, WDCM 00217, JCM 7579, CCM 3558, CNY 3953

straininfo link

  • @ref: 74716
  • straininfo: 14033

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology19505577Cloning, expression, and characterization of a new deoxyribose 5-phosphate aldolase from Yersinia sp. EA015.Kim YM, Chang YH, Choi NS, Kim Y, Song JJ, Kim JSProtein Expr Purif10.1016/j.pep.2009.06.0022009Acetaldehyde/metabolism, Aldehyde-Lyases/*biosynthesis/chemistry/genetics/metabolism, Amino Acid Sequence, Chromatography, Affinity, Escherichia coli/enzymology/genetics, Glyceraldehyde 3-Phosphate/metabolism, Histidine/genetics, Hydrogen-Ion Concentration, Molecular Sequence Data, Protein Stability, Recombinant Fusion Proteins/*biosynthesis/chemistry/genetics/metabolism, Sequence Alignment, Soil Microbiology, Temperature, Yersinia/*enzymology/genetics/isolation & purificationMetabolism
Transcriptome24116118Transcriptome changes associated with anaerobic growth in Yersinia intermedia (ATCC29909).Babujee L, Balakrishnan V, Kiley PJ, Glasner JD, Perna NTPLoS One10.1371/journal.pone.00765672013Anaerobiosis, Animals, *Gene Expression Regulation, Bacterial, *Gene Expression Regulation, Developmental, Genes, Bacterial/genetics, Humans, Oligonucleotide Array Sequence Analysis, Oxygen/metabolism/pharmacology, *Transcriptome, Yersinia/drug effects/*genetics/growth & development, Yersinia Infections/microbiologyPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7570Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18517)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18517
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
41872Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11121
45418Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 11292)https://www.ccug.se/strain?id=11292
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
74716Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14033.1StrainInfo: A central database for resolving microbial strain identifiers
120148Curators of the CIPCollection of Institut Pasteur (CIP 80.28)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2080.28