Strain identifier

BacDive ID: 10809

Type strain: Yes

Species: Nocardia coubleae

Strain history: CIP <- 2005, P. Boiron, C. Bernard Univ., Lyon, France: strain OFN N12

NCBI tax ID(s): 1210069 (strain), 356147 (species)

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General

@ref: 12213

BacDive-ID: 10809

DSM-Number: 44960

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

description: Nocardia coubleae DSM 44960 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil in the Ahmadi oil field.

NCBI tax id

NCBI tax idMatching level
1210069strain
356147species

strain history

@refhistory
12213<- P. Boiron; OFN N12 <- Z. U Khan
419812005, P. Boiron, C. Bernard Univ., Lyon, France: strain OFN N12
67770IFM 10920 <-- DSM 44960 <-- P. Boiron OFN N12 <-- Z. U. Khan.
118769CIP <- 2005, P. Boiron, C. Bernard Univ., Lyon, France: strain OFN N12

doi: 10.13145/bacdive10809.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Nocardiaceae
  • genus: Nocardia
  • species: Nocardia coubleae
  • full scientific name: Nocardia coubleae Rodríguez-Nava et al. 2007

@ref: 12213

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia coubleae

full scientific name: Nocardia coubleae Rodríguez-Nava et al. 2007

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidencecell shape
32015positive
69480no94.795
69480positive100
118769positivenorod-shaped

colony morphology

@refcolony colorincubation periodmedium used
20145Deep orange (2011)10-14 daysISP 2
20145Cream (9001)10-14 daysISP 3
20145Cream (9001)10-14 daysISP 4
20145Cream (9001)10-14 daysISP 5
20145Cream (9001)10-14 daysISP 6
20145Cream (9001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20145yesAerial MyceliumCreamISP 2
20145yesAerial MyceliumCreamISP 3
20145noISP 4
20145noISP 5
20145yesAerial MyceliumCreamISP 6
20145noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12213TRYPTICASE 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
12213GYM 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
20145ISP 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
20145ISP 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:
20145ISP 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
20145ISP 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
20145ISP 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
20145ISP 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
41981MEDIUM 129 - for Pseudonocardia, Nocardia, Skermania and Streptomyces seoulensis, Streptomyces stramineusyesDistilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (10.000g);Yeast extract (1.000 g);Beef extract (1.000 g);Casamino acids (2.000 g)
118769CIP Medium 129yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=129

culture temp

@refgrowthtypetemperaturerange
12213positivegrowth28mesophilic
32015positivegrowth25-37mesophilic
32015positiveoptimum37mesophilic
41981positivegrowth37mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
12213aerobe
32015aerobe
118769obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480no98.818

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4, ω-cycl)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2014517234glucose+
2014522599arabinose+/-
2014517992sucrose-
2014518222xylose-
2014517268myo-inositol-
2014529864mannitol-
2014528757fructose+
2014526546rhamnose-
2014516634raffinose-
2014562968cellulose-
3201528757fructose+carbon source
3201528260galactose+carbon source
3201517234glucose+carbon source
3201517754glycerol+carbon source
3201517306maltose+carbon source
3201529864mannitol+carbon source
3201537684mannose+carbon source
3201516634raffinose+carbon source
3201533942ribose+carbon source
3201517992sucrose+carbon source
11876917632nitrate+reduction
11876916301nitrite-reduction

metabolite production

  • @ref: 118769
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
118769oxidase-
118769catalase+1.11.1.6
118769urease-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+
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 zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20145++++++---++---++---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
12213soil in the Ahmadi oil fieldKuwaitKWTAsia
67770Oil-contaminated soil from the Ahmadi oilfieldKuwaitKWTAsia
118769Environment, Oil, contaminated soilKuwaitKWTAsia1997

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Oil reservoir
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_67027.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_578;97_676;98_786;99_67027&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: DQ235689
  • Sequence Identity:
  • Total samples: 54
  • soil counts: 10
  • aquatic counts: 2
  • animal counts: 12
  • plant counts: 30

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
122131Risk group (German classification)
201451German classification
1187692Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia coubleae strain DSM 44960 16S ribosomal RNA gene, partial sequenceJN041456462ena356147
20218Nocardia coubleae strain OFN N12 16S ribosomal RNA gene, partial sequenceDQ2356891322ena356147
32015Nocardia coublieae strain OFN N11 16S ribosomal RNA gene, partial sequenceDQ2356881322nuccore356147

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia coubleae NBRC 1082521210069.4wgspatric1210069
66792Nocardia coubleae strain DSM 44960356147.3wgspatric356147
66792Nocardia coubleae DSM 449602902498892draftimg356147
66792Nocardia coubleae NBRC 1082522731957729draftimg1210069
67770Nocardia coubleae NBRC 108252GCA_001612805contigncbi1210069
67770Nocardia coubleae DSM 44960GCA_012395945contigncbi356147

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.744no
gram-positiveyes88.914yes
anaerobicno99.476yes
aerobicyes93.854no
halophileno90.737no
spore-formingyes80.436no
thermophileno99.318yes
glucose-utilyes90.992no
flagellatedno97.786no
glucose-fermentno92.492no

External links

@ref: 12213

culture collection no.: DSM 44960, CIP 108996, OFN N12, JCM 15318, IFM 10920, NBRC 108252

straininfo link

  • @ref: 80073
  • straininfo: 309472

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17625180Nocardia coubleae sp. nov., isolated from oil-contaminated Kuwaiti soil.Rodriguez-Nava V, Khan ZU, Potter G, Kroppenstedt RM, Boiron P, Laurent FInt J Syst Evol Microbiol10.1099/ijs.0.64815-02007Bacterial Proteins/genetics, Bacterial Typing Techniques, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA/genetics, Heat-Shock Proteins/genetics, Kuwait, Molecular Sequence Data, Nocardia/*classification/genetics/*isolation & purification, *Petroleum, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, *Soil Pollutants, Superoxide Dismutase/geneticsGenetics
Phylogeny27510998Nocardia lasii sp. nov., a novel actinomycete isolated from the cuticle of an ant (Lasius fuliginosus L).Liu C, Bai L, Ye L, Zhao J, Yan K, Xiang W, Wang XAntonie Van Leeuwenhoek10.1007/s10482-016-0753-y2016Animals, Ants/*microbiology, DNA, Bacterial, Molecular Typing, Nocardia/classification/*isolation & purification, Phylogeny, RNA, Ribosomal, 16S/geneticsEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
12213Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44960)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44960
20145Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44960.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
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
32015Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128268
41981Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6689
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/
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
80073Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309472.1StrainInfo: A central database for resolving microbial strain identifiers
118769Curators of the CIPCollection of Institut Pasteur (CIP 108996)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108996