Strain identifier

BacDive ID: 10559

Type strain: Yes

Species: Gordonia rubripertincta

Strain history: CIP <- 1996, DSM, Gordonia rubropertinctus <- NCIB, Nocardia rubropertincta <- ATCC <- R.S. Breed <- R.E. Gordon: strain 154, Mycobacterium rubropertinctum

NCBI tax ID(s): 1077975 (strain), 36822 (species)

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General

@ref: 10861

BacDive-ID: 10559

DSM-Number: 43197

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

description: Gordonia rubripertincta DSM 43197 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1077975strain
36822species

strain history

@refhistory
10861<- NCIB (Nocardia rubropertincta) <- ATCC <- R. E. Gordon, 154 (Mycobacterium ruberpertinctum)
67770KCC A-0204 <-- M. Goodfellow N4 <-- NCIB 9664 <-- ATCC 14352 <-- R. E. Gordon 154.
122297CIP <- 1996, DSM, Gordonia rubropertinctus <- NCIB, Nocardia rubropertincta <- ATCC <- R.S. Breed <- R.E. Gordon: strain 154, Mycobacterium rubropertinctum

doi: 10.13145/bacdive10559.20230509.8.1

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 rubripertincta
  • full scientific name: Gordonia rubripertincta corrig. (Hefferan 1904) Stackebrandt et al. 1989

  • synonyms

    @refsynonym
    20215Bacillus rubropertinctus
    20215Rhodococcus corallinus
    20215Serratia corallina
    20215Rhodococcus rubropertinctus
    20215Gordona rubropertinctus
    20215Gordonia rubropertinctus
    20215Gordona rubripertincta
    20215Gordona rubra

@ref: 10861

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia rubripertincta

full scientific name: Gordonia rubripertincta (Hefferan 1904) Stackebrandt et al. 1989 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
122297positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19559Pure orange10-14 daysISP 2
19559Pure orange10-14 daysISP 3
19559Pure orange10-14 daysISP 4
19559Pure orange10-14 daysISP 5
19559Pure orange10-14 daysISP 6
19559Pure orange10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19559noISP 2
19559noISP 3
19559noISP 4
19559noISP 5
19559noISP 6
19559noISP 7

multimedia

  • @ref: 10861
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43197.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10861TRYPTICASE 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
10861GYM 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
19559ISP 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
19559ISP 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:
19559ISP 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
19559ISP 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
19559ISP 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
19559ISP 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
38669MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122297CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
10861positivegrowth28mesophilic
38669positivegrowth30mesophilic
67770positivegrowth28mesophilic
122297positivegrowth10-41
122297nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122297
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.982

compound production

@refcompound
10861mycobactin
20216Mycobactin
19559Antifungal metabolite

halophily

  • @ref: 19559
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 7.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1955917234glucose+
1955922599arabinose+
1955917992sucrose+
1955918222xylose+
1955917268myo-inositol+
1955929864mannitol+
1955928757fructose+
1955926546rhamnose+
1955916634raffinose+
1955962968cellulose+
6836817634D-glucose-fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
12229716947citrate+carbon source
1222974853esculin-hydrolysis
12229717632nitrate-reduction
12229716301nitrite-reduction
12229717632nitrate-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

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12229735581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
12229715688acetoin-
12229717234glucose-

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
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
122297oxidase-
122297beta-galactosidase-3.2.1.23
122297alcohol dehydrogenase-1.1.1.1
122297gelatinase-
122297amylase-
122297DNase-
122297caseinase-3.4.21.50
122297catalase+1.11.1.6
122297tween esterase-
122297gamma-glutamyltransferase-2.3.2.2
122297lecithinase-
122297lipase-
122297lysine decarboxylase-4.1.1.18
122297ornithine decarboxylase-4.1.1.17
122297protease-
122297tryptophan deaminase-
122297urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
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
19559-+++-++++++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19559+-+-++---++---++---
122297+++++----++---++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLU
19559----+-+-----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122297-+-----+------------------+----+-+-++------------+---+-------------+-----------++---+-----------+-+

Isolation, sampling and environmental information

isolation

@refsample type
10861soil
52416Soil
122297Environment, Soil

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5412.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_85;97_90;98_746;99_5412&stattab=map
  • Last taxonomy: Gordonia
  • 16S sequence: X80632
  • Sequence Identity:
  • Total samples: 196
  • soil counts: 28
  • aquatic counts: 44
  • animal counts: 117
  • plant counts: 7

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
108611Risk group (German classification)
195591Risk group (German classification)
1222971Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218G.rubropertinctus 16S rRNA gene (ATCC 14352T)X819151400ena36822
20218Gordonia rubripertinctus 16S rRNA gene, strain DSM43197TX806321485ena36822

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gordonia rubripertincta NBRC 1019081077975.4wgspatric1077975
66792Gordonia rubripertincta strain ATCC 1435236822.12wgspatric36822
66792Gordonia rubripertincta NBRC 1019082523231045draftimg1077975
67770Gordonia rubripertincta NBRC 101908GCA_000327325contigncbi1077975
67770Gordonia rubripertincta ATCC 14352GCA_012396225contigncbi36822

GC content

  • @ref: 67770
  • GC-content: 67.4
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno79no
motileno94.75no
flagellatedno98.686no
gram-positiveyes85.294no
anaerobicno99.49no
aerobicyes90.504no
halophileno89.566no
spore-formingno86.239no
thermophileno98.869yes
glucose-utilyes90.533no
glucose-fermentno89.626yes

External links

@ref: 10861

culture collection no.: DSM 43197, ATCC 14352, JCM 3204, KCC A-0204, NCIB 9664, CCUG 34957, LMG 5367, CIP 104661, BCRC 12520, IFM 10321, IFO 16048, IMET 7277, KCTC 9802, LMG 4083, NBRC 101908, NBRC 16048, NCIMB 9664, VKM Ac-1016, IMET 7217, ICPB 4415

straininfo link

  • @ref: 79835
  • straininfo: 2981

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10861Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43197)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43197
19559Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43197.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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
38669Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16594
52416Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 34957)https://www.ccug.se/strain?id=34957
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/
68368Automatically annotated from API 20E
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)
79835Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2981.1StrainInfo: A central database for resolving microbial strain identifiers
122297Curators of the CIPCollection of Institut Pasteur (CIP 104661)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104661