Strain identifier

BacDive ID: 5234

Type strain: No

Species: Yokenella regensburgei

Strain Designation: 3349-72

Strain history: CIP <- 1987, ATCC, Koserella trabulsii <- G. Carter, CDC: strain 3349-72 <- Georgia State Hlth. Dept., USA

NCBI tax ID(s): 158877 (species)

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General

@ref: 1926

BacDive-ID: 5234

DSM-Number: 5079

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

description: Yokenella regensburgei 3349-72 is a mesophilic, motile bacterium that was isolated from human wrist wound.

NCBI tax id

  • NCBI tax id: 158877
  • Matching level: species

strain history

@refhistory
1926<- ATCC <- G. Carter, CDC 3349-72 <- Georgia State Hlth. Dept
67770Y. Kosako <-- R. Sakazaki <-- CDC 3349-72 <-- Georgia State Health Dept., USA.
122149CIP <- 1987, ATCC, Koserella trabulsii <- G. Carter, CDC: strain 3349-72 <- Georgia State Hlth. Dept., USA

doi: 10.13145/bacdive5234.20230509.8.1

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: 1926

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Yokenella

species: Yokenella regensburgei

full scientific name: Yokenella regensburgei Kosako et al. 1985

strain designation: 3349-72

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes97.605
6948099.969negative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1926NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
35473MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122149CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
1926positivegrowth37mesophilic
35473positivegrowth30mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.896

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
6837418257ornithine+degradation
6837429016arginine+hydrolysis
6837425094lysine+degradation
6837416199urea-hydrolysis
6837418403L-arabitol-builds acid from
6837418024D-galacturonic acid+builds acid from
68374Potassium 5-ketogluconate-builds acid from
6837416899D-mannitol+builds acid from
6837417306maltose+builds acid from
6837415963ribitol-builds acid from
6837418394palatinose-builds acid from
6837415792malonate-assimilation
6837427897tryptophan-energy source
6837417634D-glucose+builds acid from
6837417992sucrose-builds acid from
6837430849L-arabinose+builds acid from
6837418333D-arabitol-builds acid from
6837427082trehalose+builds acid from
6837462345L-rhamnose+builds acid from
6837417268myo-inositol+builds acid from
6837417057cellobiose+builds acid from
6837430911sorbitol-builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
6837435581indoleno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6837435581indole-
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68374L-aspartate arylamidase-3.4.11.21
68374alpha-maltosidase-
68374alpha-galactosidase+3.2.1.22
68374alpha-glucosidase-3.2.1.20
68374beta-galactosidase+3.2.1.23
68374N-acetyl-beta-glucosaminidase-3.2.1.52
68374beta-glucuronidase-3.2.1.31
68374beta-glucosidase+3.2.1.21
68374lipase-
68374urease-3.5.1.5
68374lysine decarboxylase+4.1.1.18
68374arginine dihydrolase+3.5.3.6
68374ornithine decarboxylase+4.1.1.17
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

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
46888+++++------++--+-+++-

API ID32E

@refODCADH ArgLDC LysURELARLGAT5KGLIPRPbeta GLUMANMALADOPLEbeta GURMNTINDbeta NAGbeta GALGLUSACLARADARLalpha GLUalpha GALTRERHAINOCELSORalphaMALAspA
46888+++--+---+++------++-+--+++++---

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinent
1926human wrist wound
46888Human wrist wound1972GeorgiaUSAUSANorth America
67770Human wrist woundGAUSAUSANorth America
122149Human, Wrist wound

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Other#Wound
#Host Body-Site#Limb#Hand

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
19262Risk group (German classification)
1221491Risk group (French classification)

Sequence information

16S sequences

  • @ref: 67770
  • description: Yokenella regensburgei JCM 3958 gene for 16S ribosomal RNA, partial sequence
  • accession: LC420108
  • length: 1462
  • database: ena
  • NCBI tax ID: 158877

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Yokenella regensburgei strain DSM 5079158877.9wgspatric158877
66792Yokenella regensburgei strain NCTC12131158877.12wgspatric158877
66792Yokenella regensburgei DSM 50792757320407draftimg158877
67770Yokenella regensburgei NCTC12131GCA_900706795contigncbi158877
67770Yokenella regensburgei DSM 5079GCA_003634235scaffoldncbi158877

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.701no
gram-positiveno98.385no
anaerobicno95.564no
aerobicyes76.089no
halophileno93.529no
spore-formingno92.833no
thermophileno99.165no
glucose-utilyes95.822no
flagellatedno55.667no
glucose-fermentyes92.437yes

External links

@ref: 1926

culture collection no.: DSM 5079, ATCC 35313, CDC 3349-72, CCUG 18772, CIP 103033, NCTC 12131, LMG 7872, JCM 3958, PCM 2476

straininfo link

  • @ref: 74726
  • straininfo: 3185

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny3968202Koserella trabulsii, a new genus and species of Enterobacteriaceae formerly known as Enteric Group 45.Hickman-Brenner FW, Huntley-Carter GP, Fanning GR, Brenner DJ, Farmer JJ 3rdJ Clin Microbiol10.1128/jcm.21.1.39-42.19851985Adult, Aged, Anti-Bacterial Agents/pharmacology, DNA, Bacterial/genetics, Drug Resistance, Microbial, Enterobacteriaceae/*classification/drug effects/genetics/metabolism, Female, Humans, Male, Microbial Sensitivity Tests, Middle Aged, Nucleic Acid Hybridization, Phenotype, Terminology as TopicPathogenicity
Enzymology10512635Structures of the O-specific polysaccharides from Yokenella regensburgei (Koserella trabulsii) strains PCM 2476, 2477, 2478, and 2494: high-resolution magic-angle spinning NMR investigation of the O-specific polysaccharides in native lipopolysaccharides and directly on the surface of living bacteria.Jachymek W, Niedziela T, Petersson C, Lugowski C, Czaja J, Kenne LBiochemistry10.1021/bi990673y1999Carbohydrate Conformation, Carbohydrate Sequence, Electrophoresis, Polyacrylamide Gel, Enterobacteriaceae/*chemistry, Enzyme-Linked Immunosorbent Assay, Magnetic Resonance Spectroscopy/*methods, Molecular Sequence Data, O Antigens/*chemistry, Species Specificity, Spectrometry, Mass, Fast Atom BombardmentGenetics
19880424Structures of two novel, serologically nonrelated core oligosaccharides of Yokenella regensburgei lipopolysaccharides differing only by a single hexose substitution.Niedziela T, Jachymek W, Lukasiewicz J, Maciejewska A, Andersson R, Kenne L, Lugowski CGlycobiology10.1093/glycob/cwp1672009Carbohydrate Conformation, Enterobacteriaceae/*chemistry/cytology, Hexoses/*analysis/*chemistry, Lipopolysaccharides/*chemistry, Magnetic Resonance Spectroscopy, Mass Spectrometry, Oligosaccharides/*chemistry

Reference

@idauthorscataloguedoi/urltitle
1926Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5079)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5079
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
35473Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14785
46888Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 18772)https://www.ccug.se/strain?id=18772
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
68374Automatically annotated from API ID32E
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
74726Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3185.1StrainInfo: A central database for resolving microbial strain identifiers
122149Curators of the CIPCollection of Institut Pasteur (CIP 103033)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103033