Strain identifier

BacDive ID: 131083

Type strain: Yes

Species: Enterobacter kobei

Variant: Isotype of BacDive ID 22999

Strain history: CIP <- 1998, JCM <- Y. Kosako: strain NIH 1485-79

NCBI tax ID(s): 208224 (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 2:
version 1:
version 8.1 (current version)

General

@ref: 22375

BacDive-ID: 131083

DSM-Number: 13645

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

description: Enterobacter kobei DSM 13645 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from blood from diabetic patient.

NCBI tax id

  • NCBI tax id: 208224
  • Matching level: species

strain history

@refhistory
22375<- JCM <- R. Sakazaki <- K. Miki
67770R. Sakazaki; NIH 1485-79 <-- K. Miki.
120454CIP <- 1998, JCM <- Y. Kosako: strain NIH 1485-79

doi: 10.13145/bacdive131083.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Enterobacter
  • species: Enterobacter kobei
  • full scientific name: Enterobacter kobei Kosako et al. 1997

@ref: 22375

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Enterobacter

species: Enterobacter kobei

full scientific name: Enterobacter kobei Kosako et al. 1997 emend. Hoffmann et al. 2005

variant: Isotype of BacDive ID 22999

type strain: yes

Morphology

cell morphology

  • @ref: 120454
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
22375COLUMBIA 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
22375TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
22375positivegrowth37mesophilic
67770positivegrowth37mesophilic
120454positivegrowth10-41
120454nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120454
  • oxygen tolerance: facultative 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
68371D-lyxose-builds acid from62318
68371turanose+builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
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
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
68368L-arabinose+fermentation30849
68368amygdalin+fermentation27613
68368melibiose+fermentation28053
68368sucrose+fermentation17992
68368L-rhamnose+fermentation62345
68368sorbitol+fermentation30911
68368myo-inositol+fermentation17268
68368D-mannitol+fermentation16899
68368D-glucose+fermentation17634
68368gelatin-hydrolysis5291
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368citrate+assimilation16947
68368ornithine+degradation18257
68368lysine-degradation25094
68368arginine+hydrolysis29016
120454mannitol+fermentation29864
120454citrate+carbon source16947
120454glucose+fermentation17234
120454lactose+fermentation17716
120454nitrate+reduction17632
120454nitrite-reduction16301
120454malonate+assimilation15792
120454sodium thiosulfate-builds gas from132112
120454glucose+degradation17234

antibiotic resistance

  • @ref: 120454
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12045435581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
12045415688acetoin+
12045417234glucose-

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
120454oxidase-
120454beta-galactosidase+3.2.1.23
120454alcohol dehydrogenase+1.1.1.1
120454gelatinase-
120454catalase+1.11.1.6
120454lysine decarboxylase-4.1.1.18
120454ornithine decarboxylase+4.1.1.17
120454phenylalanine ammonia-lyase-4.3.1.24
120454tryptophan deaminase-
120454urease-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
120454-+++-+----++++--+---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
22375++-++------+++++++++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120454+--+++---++++-++-++-+++/-++/-+++++++--++/---++-------+-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120454+++++-++++++++++-+-+++++-----+-+-++++----+-++---++---++++--++--------------+---++-----+--++++++----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
22375blood from diabetic patientJapanJPNAsia
67770Blood culture from a diabetic patient

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body Product#Fluids#Blood

taxonmaps

  • @ref: 69479
  • File name: preview.99_3497.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_7;98_17;99_3497&stattab=map
  • Last taxonomy: Enterobacterales
  • 16S sequence: AB616140
  • Sequence Identity:
  • Total samples: 341
  • soil counts: 10
  • aquatic counts: 59
  • animal counts: 257
  • plant counts: 15

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
223752Risk group (German classification)
1204542Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Enterobacter kobei gene for 16S rRNA, partial sequence, strain: JCM 8580AB6161401468ena208224
18817Enterobacter kobei partial 16S rRNA gene, strain CIP 105566AJ5083011451ena208224

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Enterobacter kobei JCM 8580GCA_018323985completencbi208224
66792Enterobacter kobei DSM 13645GCA_001729765completencbi208224
66792Enterobacter kobei strain DSM 13645208224.25plasmidpatric208224
66792Enterobacter kobei strain DSM 13645208224.12completepatric208224
66792Enterobacter kobei strain JCM 8580208224.15wgspatric208224
66792Enterobacter kobei strain JCM 8580208224.167completepatric208224
66792Enterobacter kobei JCM 85802916417672draftimg208224
66792Enterobacter kobei DSM 136452721755753completeimg208224
67770Enterobacter kobei ATCC BAA-260GCA_900156385scaffoldncbi208224
67770Enterobacter kobei SJ5-8GCA_900185885contigncbi208224
67770Enterobacter kobei JCM 8580GCA_001940295scaffoldncbi208224

GC content

  • @ref: 67770
  • GC-content: 53
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno62.739no
gram-positiveno97.572no
anaerobicno96.471no
aerobicyes77.07no
halophileno90.634no
spore-formingno91.596no
thermophileno99.42no
glucose-utilyes94.434no
motileyes90.497no
glucose-fermentyes91.713yes

External links

@ref: 22375

culture collection no.: DSM 13645, CCUG 49023, JCM 8580, NIH 1485-79, ATCC BAA 260, CIP 105566, DSM 27110, VTT E-052846

straininfo link

  • @ref: 89546
  • straininfo: 46277

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny8824173Enterobacter kobei sp. nov., a new species of the family Enterobacteriaceae resembling Enterobacter cloacae.Kosako Y, Tamura K, Sakazaki R, Miki KCurr Microbiol10.1007/s0028499001101996Bacteriological Techniques, Culture Media/metabolism, DNA, Bacterial/analysis, Enterobacter/*classification/genetics/metabolism, Enterobacter cloacae/genetics/metabolism, Nucleic Acid Hybridization, PhenotypeMetabolism
29472760Genetic Diversity and Functional Analysis of Sigma Factors in Enterobacter cloacae Complex Resourced From Various Niche.Nazir F, Ibrahim M, Zaman G, Hussain A, Yar AM, Bo ZEvol Bioinform Online10.1177/11769343187548782018

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
18817Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27110)https://www.dsmz.de/collection/catalogue/details/culture/DSM-27110
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
22375Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13645)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13645
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
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
89546Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46277.1StrainInfo: A central database for resolving microbial strain identifiers
120454Curators of the CIPCollection of Institut Pasteur (CIP 105566)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105566