Strain identifier

BacDive ID: 3238

Type strain: Yes

Species: Corynebacterium pilbarense

Strain history: CCUG 57942 <-- A. F. Yassin IMMIB WACC-658.

NCBI tax ID(s): 630407 (strain), 1288393 (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: 16344

BacDive-ID: 3238

DSM-Number: 45350

keywords: 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, rod-shaped, human pathogen

description: Corynebacterium pilbarense JCM 17319 is a facultative anaerobe, mesophilic, Gram-positive human pathogen that was isolated from ankle aspirate of a 54 year old man probably with gout.

NCBI tax id

NCBI tax idMatching level
1288393species
630407strain

strain history

@refhistory
16344<- A. F. Yassin; IMMIB WACC 658
67770CCUG 57942 <-- A. F. Yassin IMMIB WACC-658.

doi: 10.13145/bacdive3238.20230509.8.1

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 pilbarense
  • full scientific name: Corynebacterium pilbarense Aravena-Roman et al. 2010

@ref: 16344

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Corynebacteriaceae

genus: Corynebacterium

species: Corynebacterium pilbarense

full scientific name: Corynebacterium pilbarense Aravena-Roman et al. 2010

type strain: yes

Morphology

cell morphology

  • @ref: 29565
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16344COLUMBIA 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
16344TRYPTICASE 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

culture temp

@refgrowthtypetemperaturerange
16344positivegrowth37mesophilic
29565positivegrowth37mesophilic
61529positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29565facultative anaerobe
61529microaerophile

spore formation

  • @ref: 29565
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2956517234glucose+carbon source
2956533942ribose+carbon source
2956517992sucrose+carbon source
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
683695291gelatin+hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
29565acid phosphatase+3.1.3.2
29565alkaline phosphatase+3.1.3.1
29565catalase+1.11.1.6
29565pyrazinamidase+3.5.1.B15
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
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382alkaline phosphatase+3.1.3.1
68369gelatinase+
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
16344-++/-----+/----+/---------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
16344------+-+/----+/-----+/-+/--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
16344ankle aspirate of a 54 year old man probably with goutPilbara RegionAustraliaAUSAustralia and Oceania
61529Human ankle aspirate,54-year old man with goutPilbara regionAustraliaAUSAustralia and Oceania2009-01-23
67770Human ankle aspirate from a 54-year-old man probably with goutPilbara, West AustraliaAustraliaAUSAustralia and Oceania

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Fluids#Aspirate
#Host#Human#Male

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: FN295567
  • Sequence Identity:
  • Total samples: 1806
  • soil counts: 13
  • aquatic counts: 36
  • animal counts: 1752
  • plant counts: 5

Safety information

risk assessment

  • @ref: 16344
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16344
  • description: Corynebacterium pilbarense DSM 45350 partial 16S rRNA gene, type strain IMMIB WACC-658T
  • accession: FN295567
  • length: 1486
  • database: ena
  • NCBI tax ID: 630407

External links

@ref: 16344

culture collection no.: JCM 17319, DSM 45350, CCUG 57942, WACC 658, IMMIB WACC 658

straininfo link

  • @ref: 72752
  • straininfo: 402125

literature

  • topic: Phylogeny
  • Pubmed-ID: 19671713
  • title: Corynebacterium pilbarense sp. nov., a non-lipophilic corynebacterium isolated from a human ankle aspirate.
  • authors: Aravena-Roman M, Sproer C, Straubler B, Inglis T, Yassin AF
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.015966-0
  • year: 2009
  • mesh: Ankle/*microbiology, Base Sequence, Corynebacterium/*classification/genetics/isolation & purification/physiology, Humans, Male, Middle Aged, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16344Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45350)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45350
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
29565Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2596028776041
61529Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 57942)https://www.ccug.se/strain?id=57942
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
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
72752Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402125.1StrainInfo: A central database for resolving microbial strain identifiers