Strain identifier

BacDive ID: 10602

Type strain: Yes

Species: Gordonia desulfuricans

Strain Designation: 213E

Strain history: CIP <- 2005, DSMZ <- M. Goodfellow, Newcastle Univ., Newcastle upon Tyne, UK: strain 213E

NCBI tax ID(s): 1223540 (strain), 89051 (species)

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General

@ref: 11789

BacDive-ID: 10602

DSM-Number: 44462

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

description: Gordonia desulfuricans 213E is a mesophilic bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
89051species
1223540strain

strain history

@refhistory
11789<- M. Goodfellow, Univ. Newcastle; 213E
67770DSM 44462 <-- M. Goodfellow 213E.
118919CIP <- 2005, DSMZ <- M. Goodfellow, Newcastle Univ., Newcastle upon Tyne, UK: strain 213E

doi: 10.13145/bacdive10602.20230509.8.1

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 desulfuricans
  • full scientific name: Gordonia desulfuricans Kim et al. 1999

@ref: 11789

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia desulfuricans

full scientific name: Gordonia desulfuricans Kim et al. 1999 emend. Nouioui et al. 2018

strain designation: 213E

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
20060Salmon orange (2012)10-14 daysISP 2
20060Ivory (1014)10-14 daysISP 3
20060Beige (1001)10-14 daysISP 4
20060Beige (1001)10-14 daysISP 5
20060Beige (1001)10-14 daysISP 6
20060Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20060noISP 2
20060noISP 3
20060noISP 4
20060noISP 5
20060noISP 6
20060noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11789TRYPTICASE 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
20060ISP 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
20060ISP 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:
20060ISP 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
20060ISP 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
20060ISP 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
20060ISP 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
36504MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118919CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
20060positiveoptimum30mesophilic
11789positivegrowth28mesophilic
36504positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2006017234glucose+
2006022599arabinose+
2006017992sucrose+
2006018222xylose-
2006017268myo-inositol-
2006029864mannitol+
2006028757fructose+
2006026546rhamnose+
2006016634raffinose-
2006062968cellulose+
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
20060--++-++--+-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20060++++++++-++++-++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11789soilScotland, West Lothian, West CalderUnited KingdomGBREurope
67770SoilWest Lothian, ScotlandUnited KingdomGBREurope
118919Environment, SoilUnited KingdomGBREurope

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_3094.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_85;97_90;98_746;99_3094&stattab=map
  • Last taxonomy: Gordonia desulfuricans
  • 16S sequence: AF101416
  • Sequence Identity:
  • Total samples: 583
  • soil counts: 73
  • aquatic counts: 143
  • animal counts: 351
  • plant counts: 16

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
117891Risk group (German classification)
200601German classification
1189191Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11789
  • description: Gordonia desulfuricans strain 213E 16S ribosomal RNA gene, partial sequence
  • accession: AF101416
  • length: 1512
  • database: ena
  • NCBI tax ID: 89051

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gordonia desulfuricans 213EGCA_010119475contigncbi89051
66792Gordonia desulfuricans NBRC 1000101223540.3wgspatric1223540
66792Gordonia desulfuricans NBRC 1000102731957553draftimg1223540
67770Gordonia desulfuricans NBRC 100010GCA_001485495contigncbi1223540

GC content

@refGC-contentmethod
1178964.1high performance liquid chromatography (HPLC)
6777063.7-64.5high performance liquid chromatography (HPLC)
6777068.1genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno95.445no
gram-positiveyes87.122no
anaerobicno99.108no
aerobicyes79.676no
halophileno92.539no
spore-formingno81.732no
thermophileno98.868yes
glucose-utilyes89.112yes
flagellatedno98.29no
glucose-fermentno87.71yes

External links

@ref: 11789

culture collection no.: DSM 44462, CIP 109045, JCM 11762, NCIMB 40816, BCRC 16388, IFM 10355, KCTC 9941, NBRC 100010

straininfo link

  • @ref: 79876
  • straininfo: 50635

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10555368Gordonia desulfuricans sp. nov., a benzothiophene-desulphurizing actinomycete.Kim SB, Brown R, Oldfield C, Gilbert SC, Goodfellow MInt J Syst Bacteriol10.1099/00207713-49-4-18451999Actinomycetales/chemistry/*classification/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thiophenes/*metabolismGenetics
Phylogeny11155977Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinomycete.Kim SB, Brown R, Oldfield C, Gilbert SC, Iliarionov S, Goodfellow MInt J Syst Evol Microbiol10.1099/00207713-50-6-20312000Actinomycetales/chemistry/*classification/genetics/isolation & purification, DNA, Ribosomal/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Sulfur/*metabolism, Thiophenes/*metabolismGenetics
Metabolism27368738Biological devulcanization of ground natural rubber by Gordonia desulfuricans DSM 44462(T) strain.Tatangelo V, Mangili I, Caracino P, Anzano M, Najmi Z, Bestetti G, Collina E, Franzetti A, Lasagni MAppl Microbiol Biotechnol10.1007/s00253-016-7691-52016Biotechnology/methods, Biotransformation, Culture Media/chemistry, Gordonia Bacterium/growth & development/*metabolism, Refuse Disposal/methods, Rubber/*metabolismBiotechnology

Reference

@idauthorscataloguedoi/urltitle
11789Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44462)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44462
20060Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44462.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
36504Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6743
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
79876Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50635.1StrainInfo: A central database for resolving microbial strain identifiers
118919Curators of the CIPCollection of Institut Pasteur (CIP 109045)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109045