Strain identifier

BacDive ID: 3224

Type strain: Yes

Species: Corynebacterium ureicelerivorans

Strain history: CCUG 53377 <-- A. F. Yassin IMMIB RIV-2301.

NCBI tax ID(s): 401472 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.3 (current version):
version 9.2:
version 9.1:
version 9:
version 8.1:
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 9.3 (current version)

General

@ref: 12300

BacDive-ID: 3224

DSM-Number: 45051

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive

description: Corynebacterium ureicelerivorans DSM 45051 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from blood culture of a patient with septicemia.

NCBI tax id

  • NCBI tax id: 401472
  • Matching level: species

strain history

@refhistory
12300<- A. F. Yassin; IMMIB RIV-2301
67770CCUG 53377 <-- A. F. Yassin IMMIB RIV-2301.

doi: 10.13145/bacdive3224.20250331.9.3

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 ureicelerivorans
  • full scientific name: Corynebacterium ureicelerivorans Yassin 2007

@ref: 12300

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium ureicelerivorans

full scientific name: Corynebacterium ureicelerivorans Yassin 2007 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
23204positiveno
125438no94.5

colony morphology

@refcolony colorincubation periodmedium usedtype of hemolysiscolony size
20160Cream (9001)10-14 daysISP 2
20160Cream (9001)10-14 daysISP 6
23204creamy2 daysColumbia bloodgamma0.1-0.3 mm

multicellular morphology

@refforms multicellular complexmedium name
20160noISP 2
20160noISP 6

multimedia

  • @ref: 12300
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45051.jpg
  • caption: Medium 693 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12300COLUMBIA 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
12300TRYPTICASE SOY BROTH AGAR+BLOOD (DSMZ Medium 535a)yeshttps://mediadive.dsmz.de/medium/535aName: TRYPTICASE SOY BROTH AGAR+BLOOD (DSMZ Medium 535a) Composition: None 50.0 g/l Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
20160ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
20160ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
23204Columbia bloodyes

culture temp

@refgrowthtypetemperature
20160positiveoptimum37
12300positivegrowth37
23204positivegrowth37
59879positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23204facultative anaerobe
59879microaerophile

spore formation

  • @ref: 23204
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2320416634raffinose-builds acid from
2320417754glycerol-builds acid from
2320428087glycogen-builds acid from
2320415443inulin-builds acid from
2320430849L-arabinose-builds acid from
2320417716lactose-builds acid from
2320417306maltose-builds acid from
2320429864mannitol-builds acid from
2320430911sorbitol-builds acid from
2320417992sucrose-builds acid from
2320427082trehalose-builds acid from
232044853esculin-hydrolysis
232045291gelatin-hydrolysis
2320417632nitrate-reduction
2320465327D-xylose+builds acid from
2320417234glucose+builds acid from
2320433942ribose+builds acid from
23204606565hippurate+hydrolysis
2320416199urea+hydrolysis
6837917992sucrose+fermentation
683795291gelatin-hydrolysis
6837916199urea-hydrolysis
683794853esculin-hydrolysis

metabolite production

  • @ref: 23204
  • Chebi-ID: 15688
  • metabolite: acetoin
  • production: yes

metabolite tests

  • @ref: 23204
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: +

enzymes

@refvalueactivityec
23204acid phosphatase+3.1.3.2
23204alkaline phosphatase+3.1.3.1
23204alpha-fucosidase-3.2.1.51
23204alpha-galactosidase-3.2.1.22
23204alpha-glucosidase-3.2.1.20
23204alpha-mannosidase-3.2.1.24
23204arginine dihydrolase-3.5.3.6
23204beta-galactosidase-3.2.1.23
23204beta-glucosidase-3.2.1.21
23204beta-glucuronidase-3.2.1.31
23204catalase+1.11.1.6
23204chymotrypsin-3.4.4.5
23204cystine arylamidase-3.4.11.3
23204cytochrome oxidase-1.9.3.1
23204esterase (C 4)-
23204esterase lipase (C 8)+
23204leucine arylamidase+3.4.11.1
23204leucine arylamidase-3.4.11.1
23204N-acetyl-beta-glucosaminidase-3.2.1.52
23204naphthol-AS-BI-phosphohydrolase+
23204pyrazinamidase+3.5.1.B15
23204pyrrolidonyl arylamidase+3.4.19.3
23204trypsin-3.4.21.4
23204valine arylamidase-
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
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382trypsin-3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
68379beta-glucosidase-3.2.1.21
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68382alpha-chymotrypsin-3.4.21.1
68379gelatinase-
68379urease-3.5.1.5
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
20160--+-------+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20160+++-+-+--++-------+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
12300blood culture of a patient with septicemiaGermanyDEUEurope
59879Human blood,septicemiaGermanyDEUEurope
67770Blood culture from a patient with signs of septicaemia

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Infection#Patient
#Infection#Patient#Blood culture

taxonmaps

  • @ref: 69479
  • File name: preview.99_5533.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_386;97_434;98_3217;99_5533&stattab=map
  • Last taxonomy: Corynebacterium
  • 16S sequence: AM397636
  • Sequence Identity:
  • Total samples: 1806
  • soil counts: 13
  • aquatic counts: 36
  • animal counts: 1752
  • plant counts: 5

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
12300yes, in single cases1Risk group (German classification)
201602German classification

Sequence information

16S sequences

  • @ref: 12300
  • description: Corynebacterium ureicelerivorans partial 16S rRNA gene, type strain IMMIB RIV-2301T
  • accession: AM397636
  • length: 1481
  • database: nuccore
  • NCBI tax ID: 401472

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Corynebacterium ureicelerivorans strain IMMIB RIV-2301401472.6plasmidpatric401472
66792Corynebacterium ureicelerivorans strain IMMIB RIV-2301401472.3completepatric401472
67770Corynebacterium ureicelerivorans IMMIB RIV-2301GCA_000747315completencbi401472

GC content

  • @ref: 67770
  • GC-content: 65.01
  • method: genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes85.977yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no92.399no
125438spore-formingspore-formingAbility to form endo- or exosporesno80.676yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no53.474yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95yes
125438motile2+flagellatedAbility to perform flagellated movementno94.5yes

External links

@ref: 12300

culture collection no.: DSM 45051, CCUG 53377, CIP 109611, JCM 15295, IMMIB RIV-2301

straininfo link

  • @ref: 72738
  • straininfo: 297510

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17551029Corynebacterium ureicelerivorans sp. nov., a lipophilic bacterium isolated from blood culture.Yassin AFInt J Syst Evol Microbiol10.1099/ijs.0.64832-02007Bacteremia/*microbiology, Bacterial Typing Techniques, Blood/*microbiology, Cell Wall/chemistry, Corynebacterium/*classification/*isolation & purification, Corynebacterium Infections/*microbiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Humans, Molecular Sequence Data, Mycolic Acids/analysis, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Urease/analysisPathogenicity
Genetics25414509Complete Genome Sequence of Corynebacterium ureicelerivorans DSM 45051, a Lipophilic and Urea-Splitting Isolate from the Blood Culture of a Septicemia Patient.Tippelt A, Albersmeier A, Brinkrolf K, Ruckert C, Fernandez-Natal I, Soriano F, Tauch AGenome Announc10.1128/genomeA.01211-142014

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12300Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45051)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45051
20160Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45051.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
23204A. F. Yassin10.1099/ijs.0.64832-0Corynebacterium ureicelerivorans sp. nov., a lipophilic bacterium isolated from blood cultureIJSEM 57: 1200-1203 200717551029
59879Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53377)https://www.ccug.se/strain?id=53377
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
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
72738Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297510.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets