Strain identifier

BacDive ID: 137687

Type strain: Yes

Species: Yokenella regensburgei

Strain Designation: DC-1, 725-83

Strain history: CIP <- 1998, JCM <- R. Sakazaki: strain 725-83 <- F. Haas: strain DC-1

NCBI tax ID(s): 911023 (strain), 158877 (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 8.1 (current version)

General

@ref: 38550

BacDive-ID: 137687

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, motile

description: Yokenella regensburgei DC-1 is a facultative anaerobe, mesophilic, motile bacterium of the family Enterobacteriaceae.

NCBI tax id

NCBI tax idMatching level
158877species
911023strain

strain history

@refhistory
67770R. Sakazaki 725-83 <-- F. Haas DC-1.
38550CIP <- 1998, JCM <- R. Sakazaki: strain 725-83 <- F. Haas: strain DC-1

doi: 10.13145/bacdive137687.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Yokenella
  • species: Yokenella regensburgei
  • full scientific name: Yokenella regensburgei Kosako et al. 1985

  • synonyms

    • @ref: 20215
    • synonym: Koserella trabulsii

@ref: 38550

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacterales

family: Enterobacteriaceae

genus: Yokenella

species: Yokenella regensburgei

strain designation: DC-1, 725-83

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.735
6948099.982negative
38550yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
38550MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
38550CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
38550CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
38550positivegrowth30mesophilic
67770positivegrowth37mesophilic
38550positivegrowth10-41
38550nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 38550
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.934

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-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
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
68371esculin-builds acid from4853
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
38550mannitol+fermentation29864
38550citrate+carbon source16947
38550glucose+fermentation17234
38550lactose-fermentation17716
38550nitrate+reduction17632
38550nitrite+reduction16301
38550malonate-assimilation15792
38550sodium thiosulfate-builds gas from132112
38550glucose+degradation17234

antibiotic resistance

  • @ref: 38550
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 38550
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
3855015688acetoin-
3855017234glucose+

enzymes

@refvalueactivityec
38550oxidase-
38550beta-galactosidase+3.2.1.23
38550alcohol dehydrogenase-1.1.1.1
38550gelatinase-
38550catalase+1.11.1.6
38550lysine decarboxylase+4.1.1.18
38550ornithine decarboxylase+4.1.1.17
38550phenylalanine ammonia-lyase-4.3.1.24
38550tryptophan deaminase-
38550urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
38550-+++-++++-++-+-+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
38550+--+++---++++-+-++---+-+/--+/-++-+-+------+----+--++/--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
38550+++++-+--++---++-+-+++-++------+++--------+-----+++--++++--+++----------++-+--+++--+--+--++++++---+

Isolation, sampling and environmental information

isolation

@refcountryorigin.countrycontinentsample typehost species
38550GermanyDEUEurope
67770Intestinal flora of insect (Pyrrhcoris apterus)Pyrrhcoris apterus
38550GermanyDEUEuropeAnimal, Intestinal flora of insect

Safety information

risk assessment

  • @ref: 38550
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
67770Yokenella regensburgei gene for 16S ribosomal RNA, partial sequenceAB5197961434ena158877
67770Yokenella regensburgei strain CIP 105435 16S ribosomal RNA gene, complete sequenceJN1753391527ena158877

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Yokenella regensburgei ATCC 49455911023.3wgspatric911023
66792Yokenella regensburgei strain NCTC11966158877.8wgspatric158877
66792Yokenella regensburgei NCTC 119662839734502draftimg158877
66792Yokenella regensburgei F. Haas DC-1, ATCC 494552588253791draftimg911023
67770Yokenella regensburgei ATCC 49455GCA_000735455contigncbi911023
67770Yokenella regensburgei NCTC11966GCA_900460805contigncbi158877

GC content

  • @ref: 67770
  • GC-content: 59
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.463no
flagellatedno58.682no
gram-positiveno98.598no
anaerobicno95.525no
halophileno92.818no
spore-formingno93.629no
thermophileno99.172yes
glucose-utilyes95.244no
aerobicyes78.627no
glucose-fermentyes93.989no

External links

@ref: 38550

culture collection no.: CIP 105435, ATCC 49455, CCRC 12225, JCM 2403, BCRC 12225, IAM 14241, NBRC 102600, NCTC 11966

straininfo link

  • @ref: 94522
  • straininfo: 42487

literature

  • topic: Phylogeny
  • Pubmed-ID: 6503024
  • title: Yokenella regensburgei gen. nov., sp. nov.: a new genus and species in the family Enterobacteriaceae.
  • authors: Kosako Y, Sakazaki R, Yoshizaki E
  • journal: Jpn J Med Sci Biol
  • DOI: 10.7883/yoken1952.37.117
  • year: 1984
  • mesh: Animals, Culture Media, DNA, Bacterial/genetics, Enterobacteriaceae/*classification/growth & development/isolation & purification, Fermentation, Humans, Nucleic Acid Hybridization, Species Specificity
  • topic2: Cultivation

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
38550Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105435Collection of Institut Pasteur (CIP 105435)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
94522Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID42487.1