Strain identifier

BacDive ID: 11148

Type strain: Yes

Species: Nocardioides daedukensis

Strain Designation: MDN22

Strain history: <- CCUG <- <- J. H. Yoon, KRIBB, Taejon, South Korea

NCBI tax ID(s): 634462 (species)

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General

@ref: 17387

BacDive-ID: 11148

DSM-Number: 23819

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

description: Nocardioides daedukensis MDN22 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from Soil around wastewater treatment plant.

NCBI tax id

  • NCBI tax id: 634462
  • Matching level: species

strain history

  • @ref: 17387
  • history: <- CCUG <- <- J. H. Yoon, KRIBB, Taejon, South Korea

doi: 10.13145/bacdive11148.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Nocardioides
  • species: Nocardioides daedukensis
  • full scientific name: Nocardioides daedukensis Yoon et al. 2010

@ref: 17387

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides daedukensis

full scientific name: Nocardioides daedukensis Yoon et al. 2010

strain designation: MDN22

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29539positive1.9 µm0.6 µmrod-shapedno
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
21372Pearl gold (1036)10-14 daysISP 2
2137210-14 daysISP 3
2137210-14 daysISP 4
2137210-14 daysISP 5
21372Ocher brown (8001)10-14 daysISP 7
21372Brown beige (1011)10-14 dayssuter with tyrosine
21372Sand yellow (1002)10-14 dayssuter without tyrosine
613517 days

multicellular morphology

@refforms multicellular complexmedium name
21372noISP 2
21372noISP 3
21372noISP 4
21372noISP 5
21372noISP 7
21372noSuter with tyrosine
21372noSuter without tyrosine

pigmentation

  • @ref: 29539
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17387TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
21372ISP 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
21372ISP 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:
21372ISP 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
21372ISP 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
21372ISP 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
21372suter with tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21372suter without tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
17387R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
29539positivegrowth04-37
29539positiveoptimum30mesophilic
61351positivegrowth30mesophilic
17387positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
29539positivegrowth06-10alkaliphile
29539positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29539aerobe
61351aerobe

spore formation

@refspore formationconfidence
29539no
69481no94
69480no99.884

halophily

@refsaltgrowthtested relationconcentration
21372NaClpositivemaximum5 %
29539NaClpositivegrowth0-9 %
29539NaClpositiveoptimum0.25 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2137217234glucose+
2137222599arabinose-
2137217992sucrose-
2137218222xylose+
2137217268myo-inositol-
2137237684mannose-
2137228757fructose-
2137226546rhamnose+
2137216634raffinose-
2137262968cellulose+
2953925115malate+carbon source
2953927082trehalose+carbon source
295394853esculin+hydrolysis
2953917632nitrate+reduction
6837917632nitrate-reduction
683794853esculin+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation
6837516199urea+hydrolysis
6837529016arginine+hydrolysis
6837518257ornithine-degradation
683754853esculin-hydrolysis
6837517634D-glucose+fermentation
6837515824D-fructose+fermentation
6837516024D-mannose+fermentation
6837517306maltose+fermentation
6837517716lactose+fermentation
6837527082trehalose-fermentation
6837516899D-mannitol-fermentation
6837516634raffinose-fermentation
6837516988D-ribose-fermentation
6837517057cellobiose-fermentation
6837517632nitrate+reduction
6837517992sucrose+fermentation
6837559640N-acetylglucosamine+fermentation
6837532528turanose+fermentation
6837522599arabinose-fermentation

antibiotic resistance

  • @ref: 68375
  • ChEBI: 28368
  • metabolite: novobiocin
  • is antibiotic: yes
  • is resistant: yes
  • resistance conc.: 1.8 µg

metabolite production

  • @ref: 68375
  • Chebi-ID: 15688
  • metabolite: acetoin
  • production: yes

metabolite tests

  • @ref: 68375
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: +

enzymes

@refvalueactivityec
29539cytochrome oxidase+1.9.3.1
68375beta-glucuronidase-3.2.1.31
68375pyrrolidonyl arylamidase-3.4.19.3
68375alkaline phosphatase+3.1.3.1
68375L-arginine arylamidase-
68375beta-galactosidase-3.2.1.23
68375beta-glucosidase-3.2.1.21
68375ornithine decarboxylase-4.1.1.17
68375arginine dihydrolase+3.5.3.6
68375urease+3.5.1.5
68379gelatinase+
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
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
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
21372-+------++/-+------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21372+/---------+/-+--------

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
17387++--+++++-----++--+-++++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
17387Soil around wastewater treatment plantTaejonRepublic of KoreaKORAsia
61351Soil around wastewater treatment plantTaejonRepublic of KoreaKORAsia2006-01-01

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Water treatment plant
#Environmental#Terrestrial#Soil

Safety information

risk assessment

  • @ref: 17387
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17387
  • description: Nocardioides daedukensis strain MDN22 16S ribosomal RNA gene, partial sequence
  • accession: FJ842646
  • length: 1475
  • database: ena
  • NCBI tax ID: 634462

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides daedukensis DSM 23819GCA_013408415contigncbi634462
66792Nocardioides daedukensis strain DSM 23819634462.3wgspatric634462
66792Nocardioides daedukensis DSM 238192844615251draftimg634462

GC content

@refGC-contentmethod
1738768.7high performance liquid chromatography (HPLC)
2953968.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno94no
gram-positiveyes92.928yes
anaerobicno98.437yes
halophileno93.994no
spore-formingno84.283yes
glucose-utilyes85.017yes
thermophileno98.964yes
flagellatedno94.57no
aerobicyes93.711yes
motileno76.799yes
glucose-fermentno88.714no

External links

@ref: 17387

culture collection no.: DSM 23819, CCUG 57505, KCTC 19601

straininfo link

  • @ref: 80397
  • straininfo: 397275

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19667373Nocardioides daedukensis sp. nov., a halotolerant bacterium isolated from soil.Yoon JH, Park S, Kang SJ, Lee JS, Lee KC, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.015354-02009Actinomycetales/classification/*genetics/isolation & purification/physiology, DNA, Bacterial/genetics, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics
Phylogeny21742819Nocardioides daejeonensis sp. nov., a denitrifying bacterium isolated from sludge in a sewage-disposal plant.Woo SG, Srinivasan S, Yang J, Jung YA, Kim MK, Lee MInt J Syst Evol Microbiol10.1099/ijs.0.033308-02011Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Denitrification, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analysisGenetics
Phylogeny24699067Nocardioides pacificus sp. nov., isolated from deep sub-seafloor sediment.Fan X, Qiao Y, Gao X, Zhang XHInt J Syst Evol Microbiol10.1099/ijs.0.059873-02014Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny27170166Nocardioides pakistanensis sp. nov., isolated from a hot water spring of Tatta Pani in Pakistan.Amin A, Ahmed I, Habib N, Abbas S, Xiao M, Hozzein WN, Li WJAntonie Van Leeuwenhoek10.1007/s10482-016-0711-82016Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Aerobiosis, Bacterial Typing Techniques, Diaminopimelic Acid/analysis, Fatty Acids/metabolism, Hot Springs/*microbiology, Nucleic Acid Hybridization, Pakistan, Phenotype, Phospholipids/metabolism, Phylogeny, Sequence Analysis, DNA, Sodium Chloride/metabolism, Water MicrobiologyMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17387Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23819)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23819
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
21372Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM23819.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
29539Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2593628776041
61351Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 57505)https://www.ccug.se/strain?id=57505
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)
68375Automatically annotated from API ID32STA
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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
80397Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397275.1StrainInfo: A central database for resolving microbial strain identifiers