Strain identifier

BacDive ID: 3142

Type strain: Yes

Species: Corynebacterium jeikeium

Strain Designation: D1076

Strain history: CIP <- 1989, NCTC <- 1985, D. Pitcher <- R.E. Weaver, CDC P.S. Riley

NCBI tax ID(s): 525262 (strain), 38289 (species)

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

@ref: 3032

BacDive-ID: 3142

DSM-Number: 7171

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, rod-shaped

description: Corynebacterium jeikeium D1076 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from blood culture.

NCBI tax id

NCBI tax idMatching level
525262strain
38289species

strain history

@refhistory
3032<- ATCC; ATCC 43734 <- NCTC; NCTC 11913 <- P. J. H. Jackman; <- R. E. Weaver; <- P. W. Riley;
67770NCTC 11913 <-- D. Pitcher A376/84 <-- R. E. Weaver.
120324CIP <- 1989, NCTC <- 1985, D. Pitcher <- R.E. Weaver, CDC P.S. Riley

doi: 10.13145/bacdive3142.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Corynebacteriaceae
  • genus: Corynebacterium
  • species: Corynebacterium jeikeium
  • full scientific name: Corynebacterium jeikeium Jackman et al. 1988

@ref: 3032

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium jeikeium

full scientific name: Corynebacterium jeikeium Jackman et al. 1988 emend. Nouioui et al. 2018

strain designation: D1076

type strain: yes

Morphology

cell morphology

  • @ref: 120324
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 120324

multimedia

@refmultimedia contentintellectual property rightscaption
3032https://www.dsmz.de/microorganisms/photos/DSM_7171-1.jpg© Leibniz-Institut DSMZ
3032https://www.dsmz.de/microorganisms/photos/DSM_7171.jpg© Leibniz-Institut DSMZMedium 693 37°C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3032TRYPTICASE 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
3032COLUMBIA 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
40638MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
120324CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
3032positivegrowth37mesophilic
40638positivegrowth37mesophilic
48679positivegrowth37mesophilic
67770positivegrowth37mesophilic
120324positivegrowth30-41
120324nogrowth10psychrophilic
120324nogrowth15psychrophilic
120324nogrowth25mesophilic
120324nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
48679microaerophile
120324obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
120324NaClpositivegrowth0-6 %
120324NaClnogrowth8 %
120324NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12032416947citrate-carbon source
1203244853esculin-hydrolysis
120324606565hippurate+hydrolysis
12032417632nitrate-reduction
12032416301nitrite-reduction
12032417632nitrate-respiration
6837916199urea-hydrolysis
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917716lactose-fermentation
6837717634D-glucose+builds acid from
6837715824D-fructose-builds acid from
6837717306maltose+builds acid from
6837717992sucrose-builds acid from
6837718257ornithine-degradation
6837716199urea-hydrolysis
6837727897tryptophan-energy source

antibiotic resistance

  • @ref: 120324
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6837735581indoleno
12032435581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6837735581indole-
12032415688acetoin-
12032417234glucose-

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
68377tryptophan deaminase-4.1.99.1
68377gamma-glutamyltransferase-2.3.2.2
68377proline-arylamidase+3.4.11.5
68377beta-galactosidase-3.2.1.23
68377alkaline phosphatase+3.1.3.1
68377lipase+
68377urease-3.5.1.5
68377ornithine decarboxylase-4.1.1.17
68377beta-lactamase-3.5.2.6
68379catalase+1.11.1.6
68379urease-3.5.1.5
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase+3.5.1.B15
120324oxidase-
120324beta-galactosidase-3.2.1.23
120324alcohol dehydrogenase-1.1.1.1
120324gelatinase-
120324amylase-
120324DNase-
120324caseinase-3.4.21.50
120324catalase+1.11.1.6
120324tween esterase-
120324gamma-glutamyltransferase-2.3.2.2
120324lecithinase-
120324lipase-
120324lysine decarboxylase-4.1.1.18
120324ornithine decarboxylase-4.1.1.17
120324protease-
120324urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlGLURIBXYLMANMALLACSACGLYGCAT
3032-+-+---+/-----+/-+/-------+
3032-+-+--------++/-------+
3032++-+---++-+-++--+-+++
3032-+-+--------++/-------+

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120324-+-+------++--------

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
48679-+-+---++-+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120324---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
3032blood culture
48679Human blood
67770Blood
120324Human, BloodUnited States of AmericaUSANorth America

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
30322Risk group (German classification)
1203242Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Corynebacterium jeikeium 16S ribosomal RNA gene, complete sequenceU878231466ena38289
20218C.jeikeium 16S ribosomal DNAX820621333ena38289
20218Corynebacterium jeikeium gene for 16S rRNA, partial sequenceAB470615545ena38289
20218Corynebacterium jeikeium 16S rRNA gene, strain NCTC 11913X842501494ena38289

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium jeikeium ATCC 43734525262.3wgspatric525262
66792Corynebacterium jeikeium strain ATCC 4373438289.35wgspatric38289
66792Corynebacterium jeikeium strain NCTC1191338289.53wgspatric38289
66792Corynebacterium jeikeium ATCC 43734647000231draftimg525262
66792Corynebacterium jeikeium NCTC 119132916410081draftimg38289
67770Corynebacterium jeikeium ATCC 43734GCA_000163435scaffoldncbi525262
67770Corynebacterium jeikeium ATCC 43734GCA_001999385scaffoldncbi38289
67770Corynebacterium jeikeium NCTC11913GCA_900461185contigncbi38289
66792Corynebacterium jeikeium DSM 7171GCA_028609885completencbi38289

GC content

@refGC-contentmethod
6777061.6genome sequence analysis
6777060.1thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno94.838no
flagellatedno97.323no
gram-positiveyes93.072no
anaerobicno98.61yes
aerobicno80.837yes
halophileyes52.527no
spore-formingno91.209no
glucose-fermentno68.026no
thermophileno96.293yes
glucose-utilyes82.694no

External links

@ref: 3032

culture collection no.: DSM 7171, ATCC 43734, CIP 103337, DSM 46361, IFO 15298, IMET 11513, NBRC 15298, NCTC 11913, CCUG 27192, LMG 19049, JCM 9384, NCIMB 14491

straininfo link

  • @ref: 72659
  • straininfo: 12969

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics25116839Whole genome sequencing indicates Corynebacterium jeikeium comprises 4 separate genomospecies and identifies a dominant genomospecies among clinical isolates.Salipante SJ, Sengupta DJ, Cummings LA, Robinson A, Kurosawa K, Hoogestraat DR, Cookson BTInt J Med Microbiol10.1016/j.ijmm.2014.07.0032014Cluster Analysis, Corynebacterium/*classification/*genetics/isolation & purification/physiology, Corynebacterium Infections/*microbiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA-Directed RNA Polymerases/genetics, *Genome, Bacterial, Genotype, Humans, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPhylogeny
Phylogeny33427608Corynebacterium anserum sp. nov., isolated from the faeces of greater white-fronted geese (Anser albifrons) at Poyang Lake, PR China.Liu Q, Wu K, Fan G, Bai X, Yang X, Pan Y, Cao L, Song W, Chen S, Xiong Y, Chen HInt J Syst Evol Microbiol10.1099/ijsem.0.0046372021Animals, Bacterial Typing Techniques, Base Composition, China, Corynebacterium/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Geese/*microbiology, Lakes, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3032Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7171)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7171
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
40638Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15124
48679Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 27192)https://www.ccug.se/strain?id=27192
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/
68377Automatically annotated from API NH
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
72659Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12969.1StrainInfo: A central database for resolving microbial strain identifiers
120324Curators of the CIPCollection of Institut Pasteur (CIP 103337)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103337