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Strain identifier

BacDive ID: 5222

Type strain: Yes

Species: Yersinia frederiksenii

Strain history: 1980, H.H. Mollaret, Inst. Pasteur, Paris, France: strain CNY 6175

NCBI tax ID(s): 349966 (strain), 29484 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 7559

BacDive-ID: 5222

DSM-Number: 18490

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

description: Yersinia frederiksenii DSM 18490 is an aerobe, mesophilic bacterium that was isolated from sewage.

NCBI tax id

NCBI tax idMatching level
29484species
349966strain

strain history

doi: 10.13145/bacdive5222.20221219.7.1

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 frederiksenii
  • full scientific name: Yersinia frederiksenii Ursing et al. 1981

@ref: 7559

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Yersiniaceae

genus: Yersinia

species: Yersinia frederiksenii

full scientific name: Yersinia frederiksenii Ursing et al. 1981

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes72.288
6948099.196negative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7559TRYPTICASE 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
37716MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)

culture temp

@refgrowthtypetemperaturerange
7559positivegrowth30mesophilic
37716positivegrowth30mesophilic
45419positivegrowth30-37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 45419
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 94.362

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 95.217

fatty acid profile

  • @reffatty acidpercentageECL
    45419C12:05.612
    45419C14:01.114
    45419C15:00.715
    45419C16:031.716
    45419C17:00.217
    45419C18:00.618
    45419C12:0 2OH0.613.178
    45419C12:0 ALDE ?0.210.915
    45419C13:0 ISO 2OH0.113.814
    45419C14:0 3OH/C16:1 ISO I8.515.485
    45419C16:1 ω5c0.215.908
    45419C16:1 ω7c8.615.819
    45419C17:0 CYCLO29.816.888
    45419C17:1 ω7c0.216.818
    45419C18:1 ω7c /12t/9t7.917.824
    45419C19:0 CYCLO ω8c218.9
    45419C19:0 ISO0.418.633
    45419unknown 13.9610.713.961
    45419unknown 14.5030.714.503
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG
  • @reffatty acidpercentageECL
    45419C12:012.512
    45419C14:02.114
    45419C16:02116
    45419C12:0 ALDE ?1.910.915
    45419C14:0 3OH/C16:1 ISO I11.815.485
    45419C16:1 ω7c32.915.819
    45419C17:0 CYCLO11.516.888
    45419C18:1 ω7c /12t/9t6.317.824
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling date
7559sewageDenmarkDNKEurope
45419SewageDenmarkDNKEurope1980

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Wastewater

Safety information

risk assessment

  • @ref: 7559
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Yersinia frederiksenii strain ATCC 33641 16S ribosomal RNA gene, partial sequenceAY332818481ena349966
20218Yersinia frederiksenii strain CCUG 11293 16S ribosomal RNA gene, partial sequenceEF1791221461ena29484
7559Yersinia frederiksenii 16S ribosomal RNA gene, partial sequenceAF3663791461ena349966

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Yersinia frederiksenii ATCC 33641 ATCC 33641GCA_000754805scaffoldncbi349966
66792Yersinia frederiksenii NCTC11470GCA_900460425contigncbi29484
66792Yersinia frederiksenii ATCC 33641 ATCC 33641GCA_000168015contigncbi349966
66792Yersinia frederiksenii ATCC 33641349966.5wgspatric349966
66792Yersinia frederiksenii ATCC 33641349966.8wgspatric349966
66792Yersinia frederiksenii strain NCTC1147029484.45wgspatric29484
66792Yersinia frederiksenii ATCC 33641638341239draftimg349966
66792Yersinia frederiksenii ATCC 336412617271017draftimg349966

External links

@ref: 7559

culture collection no.: DSM 18490, ATCC 33641, CCUG 11293, CIP 80.29, NCTC 11470, CIP 8029, CNY 6175

straininfo link

@refpassport
20218http://www.straininfo.net/strains/691338
20218http://www.straininfo.net/strains/42386
20218http://www.straininfo.net/strains/42388
20218http://www.straininfo.net/strains/231524
20218http://www.straininfo.net/strains/42393

literature

Pubmed-IDtitleauthorsjournalDOIyeartopic
22567337A Novel msDNA (Multicopy Single-Stranded DNA) Strain Present in Yersinia frederiksenii ATCC 33641 Contig01029 Enteropathogenic Bacteria with the Genomic Analysis of It's Retron.Das R, Shimamoto T, Arifuzzaman MJ Pathog10.4061/2011/6937692011
34603680Genomics-driven discovery of chiral triscatechol siderophores with enantiomeric Fe(iii) coordination.Stow PR, Reitz ZL, Johnstone TC, Butler AChem Sci10.1039/d1sc03541j2021Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7559Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18490)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18490
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
37716Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11122
45419Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 11293)https://www.ccug.se/strain?id=11293
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)
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)