Strain identifier

BacDive ID: 10612

Type strain: Yes

Species: Gordonia defluvii

Strain Designation: J4

Strain history: CIP <- 2006, DSMZ <- A.L. Jones <- J.A. Soddell, La Trobe Univ., Bendigo, Victoria, Australia: strain J4

NCBI tax ID(s): 283718 (species)

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General

@ref: 12139

BacDive-ID: 10612

DSM-Number: 44981

keywords: 16S sequence, Bacteria, mesophilic

description: Gordonia defluvii J4 is a mesophilic bacterium that was isolated from activated sludge foams.

NCBI tax id

  • NCBI tax id: 283718
  • Matching level: species

strain history

@refhistory
12139<- A. L. Jones; J4 <- J. A. Soddell
67770IFM 10751 <-- DSM 44981 <-- A. L. Jones J4 <-- J. A. Soddell.
118868CIP <- 2006, DSMZ <- A.L. Jones <- J.A. Soddell, La Trobe Univ., Bendigo, Victoria, Australia: strain J4

doi: 10.13145/bacdive10612.20230509.8.1

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 defluvii
  • full scientific name: Gordonia defluvii Soddell et al. 2006

@ref: 12139

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia defluvii

full scientific name: Gordonia defluvii Soddell et al. 2006

strain designation: J4

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
19897Brown beige10-14 daysISP 2
19897Lemon yellow10-14 daysISP 3
1989710-14 daysISP 4
19897Rape yellow10-14 daysISP 5
19897Beige10-14 daysISP 6
19897Beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19897noISP 2
19897noISP 3
19897noISP 4
19897noISP 5
19897noISP 6
19897noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12139TRYPTICASE 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
12139GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
19897ISP 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
19897ISP 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:
19897ISP 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
19897ISP 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
19897ISP 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
19897ISP 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
118868CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
12139positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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

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
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19897---+--+----------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19897+++++----++---++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12139activated sludge foamsVictoria, Brimbank ParkAustraliaAUSAustralia and Oceania
67770Foam sample from an activated sludge plantBrimbank Park, VictoriaAustraliaAUSAustralia and Oceania
118868Environment, Activated sludge foamsAustraliaAUSAustralia and Oceania

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Activated sludge
#Environmental#Aquatic#Foam

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
121391Risk group (German classification)
198971Risk group (German classification)
1188681Risk group (French classification)

Sequence information

16S sequences

  • @ref: 12139
  • description: Gordonia defluvii strain J4 16S ribosomal RNA gene, partial sequence
  • accession: AY650265
  • length: 1520
  • database: ena
  • NCBI tax ID: 283718

GC content

@refGC-contentmethod
1213963.1
6777063.1high performance liquid chromatography (HPLC)

External links

@ref: 12139

culture collection no.: DSM 44981, CIP 109401, NCIMB 14149, JCM 14234, IFM 10751, NBRC 110695

straininfo link

  • @ref: 79885
  • straininfo: 297193

literature

  • topic: Phylogeny
  • Pubmed-ID: 17012545
  • title: Gordonia defluvii sp. nov., an actinomycete isolated from activated sludge foam.
  • authors: Soddell JA, Stainsby FM, Eales KL, Seviour RJ, Goodfellow M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64034-0
  • year: 2006
  • mesh: Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Gordonia Bacterium/chemistry/*classification/genetics/*isolation & purification, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
12139Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44981)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44981
19897Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44981.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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
79885Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297193.1StrainInfo: A central database for resolving microbial strain identifiers
118868Curators of the CIPCollection of Institut Pasteur (CIP 109401)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109401