Strain identifier

BacDive ID: 10603

Type strain: Yes

Species: Gordonia westfalica

Strain Designation: ID 3752, Kb 2

Strain history: CIP <- 2002, DSMZ <- A. Steinbüchel: strain Kb 2

NCBI tax ID(s): 1305624 (strain), 158898 (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: 11601

BacDive-ID: 10603

DSM-Number: 44215

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

description: Gordonia westfalica ID 3752 is an aerobe, mesophilic bacterium that was isolated from fouling tire water on a farmer's field.

NCBI tax id

NCBI tax idMatching level
158898species
1305624strain

strain history

@refhistory
11601<- A. Steinbüchel, Kb 2
67770DSM 44215 <-- A. Steinbüchel Kb2.
123948CIP <- 2002, DSMZ <- A. Steinbüchel: strain Kb 2

doi: 10.13145/bacdive10603.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Gordoniaceae
  • genus: Gordonia
  • species: Gordonia westfalica
  • full scientific name: Gordonia westfalica Linos et al. 2002

@ref: 11601

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia westfalica

full scientific name: Gordonia westfalica Linos et al. 2002 emend. Nouioui et al. 2018

strain designation: ID 3752, Kb 2

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no94.126
6948099.448positive
123948nopositiveoval-shaped

colony morphology

@refcolony colorincubation periodmedium used
20019Pastel yellow (1034)10-14 daysISP 2
20019Beige (1001)10-14 daysISP 3
20019Beige (1001)10-14 daysISP 4
20019Beige (1001)10-14 daysISP 5
20019Beige (1001)10-14 daysISP 6
20019Beige (1001)10-14 daysISP 7
123948

multicellular morphology

@refforms multicellular complexmedium name
20019noISP 2
20019noISP 3
20019noISP 4
20019noISP 5
20019noISP 6
20019noISP 7

multimedia

  • @ref: 11601
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44215.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11601TRYPTICASE 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
20019ISP 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
20019ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
20019ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
20019ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
20019ISP 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
20019ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
40562MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123948CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
20019positiveoptimum28mesophilic
11601positivegrowth28mesophilic
40562positivegrowth30mesophilic
57406positivegrowth30-37mesophilic
67770positivegrowth28mesophilic
123948positivegrowth25-41
123948nogrowth10psychrophilic
123948nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
57406aerobe
123948obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.999

halophily

@refsaltgrowthtested relationconcentration
123948NaClpositivegrowth0-8 %
123948NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2001917234glucose-
2001922599arabinose-
2001917992sucrose+
2001918222xylose-
2001917268myo-inositol-
2001929864mannitol+
2001928757fructose+
2001926546rhamnose-
2001916634raffinose-
2001962968cellulose+
12394816947citrate-carbon source
1239484853esculin-hydrolysis
123948606565hippurate-hydrolysis
12394817632nitrate+reduction
12394816301nitrite-reduction
12394817632nitrate-respiration
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

antibiotic resistance

  • @ref: 123948
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 123948
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12394815688acetoin-
12394817234glucose-

enzymes

@refvalueactivityec
68379gelatinase-
68379urease+3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
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
123948oxidase-
123948beta-galactosidase-3.2.1.23
123948alcohol dehydrogenase-1.1.1.1
123948gelatinase-
123948amylase-
123948DNase-
123948caseinase-3.4.21.50
123948catalase+1.11.1.6
123948tween esterase-
123948gamma-glutamyltransferase-2.3.2.2
123948lecithinase-
123948lipase-
123948lysine decarboxylase-4.1.1.18
123948ornithine decarboxylase-4.1.1.17
123948phenylalanine ammonia-lyase-4.3.1.24
123948protease-
123948tryptophan deaminase-
123948urease+3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382alpha-chymotrypsin-3.4.21.1
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20019---+--+--+---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20019--+-++++--+---++---
123948-++-+++--++---++----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123948-+-+---+------------------+------+--+------------+---+-------+-----+------------++------+-------+-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
11601fouling tire water on a farmer's fieldMünsterGermanyDEUEurope
57406Foul water inside an automobile tireWestfalia,farmer's fieldGermanyDEUEurope
67770Foul water inside a deteriorated tyre on a farmer's fieldWestfaliaGermanyDEUEurope
123948Environment, Fouling tire water on a farmer's fieldMünsterGermanyDEUEurope1996

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_952.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_85;97_90;98_746;99_952&stattab=map
  • Last taxonomy: Gordonia
  • 16S sequence: AJ312907
  • Sequence Identity:
  • Total samples: 706
  • soil counts: 155
  • aquatic counts: 238
  • animal counts: 301
  • plant counts: 12

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
116011Risk group (German classification)
200191German classification
1239481Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11601
  • description: Gordonia westfalica partial 16S rRNA gene, strain Kb1/Kb2
  • accession: AJ312907
  • length: 1478
  • database: ena
  • NCBI tax ID: 158898

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gordonia westfalica JCM 11757GCA_001313785contigncbi1305624
66792Gordonia westfalica JCM 117571305624.4wgspatric1305624
66792Gordonia westfalica strain DSM 44215158898.7wgspatric158898
66792Gordonia westfalica strain type strain: DSM 44215158898.6plasmidpatric158898
66792Gordonia westfalica JCM 117572675903634draftimg1305624
66792Gordonia westfalica DSM 442152636416072draftimg158898
67770Gordonia westfalica DSM 44215GCA_900105725contigncbi158898

GC content

  • @ref: 67770
  • GC-content: 66.9
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno61no
motileno91.598no
gram-positiveyes84.635no
anaerobicno99.319no
halophileno84.576no
spore-formingno93.515no
thermophileno99.497no
glucose-utilyes87.868yes
aerobicyes93.28yes
flagellatedno98.869no
glucose-fermentno91.423yes

External links

@ref: 11601

culture collection no.: DSM 44215, JCM 11757, NRRL B-24152, CCUG 46924, CIP 107642, IFM 10629, KCTC 9954, NBRC 108237

straininfo link

  • @ref: 79877
  • straininfo: 100663

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12148617Gordonia westfalica sp. nov., a novel rubber-degrading actinomycete.Linos A, Berekaa MM, Steinbuchel A, Kim KK, Sproer C, Kroppenstedt RMInt J Syst Evol Microbiol10.1099/00207713-52-4-11332002Actinomycetales/classification, *Automobiles, Bacterial Typing Techniques, Biodegradation, Environmental, Butadienes/metabolism, DNA, Ribosomal/analysis, Fatty Acids/analysis, Gordonia Bacterium/chemistry/*classification/genetics/physiology, *Hemiterpenes, Molecular Sequence Data, Nucleic Acid Hybridization, *Pentanes, Phylogeny, RNA, Ribosomal, 16S/genetics, Rubber/*metabolism, Sequence Analysis, DNAMetabolism
Phylogeny15774645Gordonia nitida Yoon et al. 2000 is a later synonym of Gordonia alkanivorans Kummer et al. 1999.Arenskotter M, Linos A, Schumann P, Kroppenstedt RM, Steinbuchel AInt J Syst Evol Microbiol10.1099/ijs.0.63400-02005DNA, Bacterial/analysis/*genetics, Deoxyribonucleases, Type II Site-Specific, Gordonia Bacterium/*classification/*genetics, Nucleic Acid Hybridization, Phylogeny, Ribotyping, Species Specificity

Reference

@idauthorscataloguedoi/urltitle
11601Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44215)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44215
20019Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44215.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
40562Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5100
57406Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 46924)https://www.ccug.se/strain?id=46924
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/
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
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)
79877Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100663.1StrainInfo: A central database for resolving microbial strain identifiers
123948Curators of the CIPCollection of Institut Pasteur (CIP 107642)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107642