Strain identifier

BacDive ID: 10619

Type strain: Yes

Species: Gordonia cholesterolivorans

Strain Designation: Chol-3

Strain history: CIP <- 2009, O. Drzyzga, Madrid Compl. Univ., Madrid, Spain: strain Chol-3

NCBI tax ID(s): 559625 (species)

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General

@ref: 15808

BacDive-ID: 10619

DSM-Number: 45229

keywords: 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive, rod-shaped

description: Gordonia cholesterolivorans Chol-3 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from sewage sludge from sewage treatment plant.

NCBI tax id

  • NCBI tax id: 559625
  • Matching level: species

strain history

@refhistory
15808<- O. Drzyzga, Universitiy of Madrid; Chol-3
67770CECT 7408 <-- O. Drzyzga Chol-3.
118253CIP <- 2009, O. Drzyzga, Madrid Compl. Univ., Madrid, Spain: strain Chol-3

doi: 10.13145/bacdive10619.20230509.8.1

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 cholesterolivorans
  • full scientific name: Gordonia cholesterolivorans Drzyzga et al. 2009

@ref: 15808

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia cholesterolivorans

full scientific name: Gordonia cholesterolivorans Drzyzga et al. 2009

strain designation: Chol-3

type strain: yes

Morphology

cell morphology

  • @ref: 118253
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
20185Beige (1001)10-14 daysISP 2
2018510-14 daysISP 3
20185Beige (1001)10-14 daysISP 4
20185Beige (1001)10-14 daysISP 5
20185Beige (1001)10-14 daysISP 6
20185Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20185noISP 2
20185noISP 3
20185noISP 4
20185noISP 5
20185noISP 6
20185noISP 7

multimedia

  • @ref: 15808
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45229.jpg
  • caption: Medium 215 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15808BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
15808GYM 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
15808TRYPTICASE 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
20185ISP 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
20185ISP 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:
20185ISP 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
20185ISP 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
20185ISP 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
20185ISP 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
37917MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118253CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
118253CIP Medium 368yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=368

culture temp

@refgrowthtypetemperaturerange
15808positivegrowth28mesophilic
20185positiveoptimum28mesophilic
37917positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118253
  • oxygen tolerance: obligate aerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11825317632nitrate+reduction
11825316301nitrite-reduction
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

metabolite production

  • @ref: 118253
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
118253oxidase-
118253catalase+1.11.1.6
118253urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
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
20185--++--+----------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20185+++++++--++---++---
118253++++++---++---++----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
15808sewage sludge from sewage treatment plantCiudad RealSpainESPEurope
67770Sewage sludge from a wastewater treatment plantCiudad RealSpainESPEurope
118253Environment, Sewage sludge sampleCiudad Real, MadridSpainESPEurope2006

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Sewage sludge
#Engineered#Waste#Water treatment plant

taxonmaps

  • @ref: 69479
  • File name: preview.99_2948.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_85;97_1820;98_2276;99_2948&stattab=map
  • Last taxonomy: Gordonia
  • 16S sequence: EU244645
  • Sequence Identity:
  • Total samples: 1008
  • soil counts: 85
  • aquatic counts: 620
  • animal counts: 263
  • plant counts: 40

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
158081Risk group (German classification)
1182531Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15808
  • description: Gordonia cholesterolivorans strain Chol-3 16S ribosomal RNA gene, partial sequence
  • accession: EU244645
  • length: 1445
  • database: ena
  • NCBI tax ID: 559625

External links

@ref: 15808

culture collection no.: DSM 45229, CECT 7408, JCM 16227, CIP 110048

straininfo link

  • @ref: 79891
  • straininfo: 362793

literature

  • topic: Phylogeny
  • Pubmed-ID: 19406784
  • title: Gordonia cholesterolivorans sp. nov., a cholesterol-degrading actinomycete isolated from sewage sludge.
  • authors: Drzyzga O, Navarro Llorens JM, Fernandez de Las Heras L, Garcia Fernandez E, Perera J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.005777-0
  • year: 2009
  • mesh: Bacterial Typing Techniques, Biodegradation, Environmental, Cholesterol/*metabolism, DNA, Bacterial/analysis/genetics, Fatty Acids/analysis, Genes, rRNA, Genotype, Gordonia Bacterium/*classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Mycolic Acids/analysis, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
15808Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45229)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45229
20185Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45229.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
37917Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7862
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
79891Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID362793.1StrainInfo: A central database for resolving microbial strain identifiers
118253Curators of the CIPCollection of Institut Pasteur (CIP 110048)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110048