Strain identifier

BacDive ID: 5222

Type strain: Yes

Species: Yersinia frederiksenii

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

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

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General

@ref: 7559

BacDive-ID: 5222

DSM-Number: 18490

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

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

NCBI tax id

NCBI tax idMatching level
349966strain
29484species

strain history

@refhistory
7559<- CIP <- H. H. Mollaret, Institut Pasteur, Paris; CNY 6175
377161980, H.H. Mollaret, Inst. Pasteur, Paris, France: strain CNY 6175
119449CIP <- 1980, H.H. Mollaret, Inst. Pasteur, Paris, France: strain CNY 6175

doi: 10.13145/bacdive5222.20230509.8.1

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 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

  • @ref: 119449
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 119449

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)
119449CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7559positivegrowth30mesophilic
37716positivegrowth30mesophilic
45419positivegrowth30-37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
45419aerobe
119449facultative 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
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
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
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
119449nitrate+reduction17632
119449nitrite-reduction16301

metabolite production

  • @ref: 119449
  • 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
119449oxidase-
119449alcohol dehydrogenase-1.1.1.1
119449catalase+1.11.1.6
119449lysine decarboxylase-4.1.1.18
119449ornithine decarboxylase+4.1.1.17
119449urease+3.5.1.5

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

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119449-++--++++-++-+-+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119449+--+++---++++++-+++--++/-++++++-++------+-+/---++-+-+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling date
7559sewageDenmarkDNKEurope
45419SewageDenmarkDNKEurope1980
119449Environment, SewageDenmarkDNKEurope

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
75592Risk group (German classification)
1194492Risk group (French 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 33641GCA_000754805scaffoldncbi349966
66792Yersinia frederiksenii NCTC11470GCA_900460425contigncbi29484
66792Yersinia frederiksenii 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

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes90.1no
flagellatedyes60.057no
gram-positiveno98.603no
anaerobicno96.443yes
aerobicyes88.759yes
halophileno93.949no
spore-formingno94.252no
glucose-utilyes94.388no
thermophileno99.12yes
glucose-fermentyes93.154no

External links

@ref: 7559

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

straininfo link

  • @ref: 74714
  • straininfo: 10838

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)
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
74714Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10838.1StrainInfo: A central database for resolving microbial strain identifiers
119449Curators of the CIPCollection of Institut Pasteur (CIP 80.29)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2080.29