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BacDive ID 11142
Type strain
Strain Designation MSL-09
Culture col. no. DSM 19266 KCTC 19272 MSL-09 JCM 16022 MSL 09
NCBI tax ID(s) 433651
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 10 (current version):
version 10 (current version)

General

@ref: 7985

BacDive-ID: 11142

DSM-Number: 19266

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

description: Nocardioides koreensis MSL-09 is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from soil, farming field.

NCBI tax id

  • NCBI tax id: 433651
  • Matching level: species

strain history

@refhistory
7985<- Chang-Jin Kim; MSL-09
67770KCTC 19272 <-- C.-J. Kim MSL-09.
67771<- CJ Kim, KRIBB

doi: 10.13145/bacdive11142.20251217.10

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: kingdom/bacillati
  • keyword: phylum/actinomycetota
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Nocardioides
  • species: Nocardioides koreensis
  • full scientific name: Nocardioides koreensis Dastager et al. 2008

@ref: 7985

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides koreensis

full scientific name: Nocardioides koreensis Dastager et al. 2008

strain designation: MSL-09

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
32484positive0.8-3.2 µm0.2-0.7 µmrod-shapedyes
67771positive

colony morphology

@refcolony colorincubation periodmedium used
19779Light ivory (1015)10-14 daysISP 2
19779Light ivory (1015)10-14 daysISP 3
19779Light ivory (1015)10-14 daysISP 4
1977910-14 daysISP 5
19779Light ivory (1015)10-14 daysISP 6
1977910-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19779noISP 2
19779noISP 3
19779noISP 4
19779noISP 5
19779noISP 6
19779noISP 7

pigmentation

  • @ref: 32484
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7985R2A 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
19779ISP 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
19779ISP 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:
19779ISP 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
19779ISP 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
19779ISP 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
19779ISP 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

culture temp

@refgrowthtypetemperature
7985positivegrowth28
19779positiveoptimum28
32484positivegrowth27-37
32484positiveoptimum30
67770positivegrowth28
67771positivegrowth30

culture pH

@refabilitytypepH
32484positivegrowth07-08
32484positiveoptimum07-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32484aerobe
67771aerobe

spore formation

  • @ref: 32484
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
32484NaClpositivegrowth0-5 %
32484NaClpositiveoptimum0-5 %

observation

@refobservation
32484aggregates in chains
67770quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3248417716lactose+carbon source
3248437684mannose+carbon source
3248428053melibiose+carbon source
6837917716lactose+fermentation
6837917992sucrose+fermentation
683795291gelatin-hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
683794853esculin-hydrolysis
6837916199urea+hydrolysis
6837928087glycogen-fermentation
6837917306maltose+fermentation
6837917632nitrate+reduction

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
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
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+
68382alkaline phosphatase+3.1.3.1
68379beta-glucosidase-3.2.1.21
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68382alpha-galactosidase-3.2.1.22
68382esterase (C 4)+
68379gelatinase-
68379urease+3.5.1.5
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase+3.2.1.23
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19779+--+-+---+-+---+++-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19779+++------++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7985soil, farming fieldBigeum IslandRepublic of KoreaKORAsia
67770SoilBigeum IslandRepublic of KoreaKORAsia
67771From farming fieldBikeum islandRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil

Interaction and safety

risk assessment

@refbiosafety levelbiosafety level comment
79851Risk group (German classification)
197791Risk group (German classification)

Sequence information

Genome sequences

  • @ref: 124043
  • description: ASM3953177v1 assembly for Nocardioides koreensis JCM 16022
  • assembly level: contig
  • INSDC accession: GCA_039531775
  • NCBI tax ID: 433651
  • score: 70.36

16S sequences

  • @ref: 7985
  • description: Nocardioides sp. MSL 09 16S ribosomal RNA gene, partial sequence
  • accession: EF466115
  • length: 1398
  • database: nuccore
  • NCBI tax ID: 433651

GC content

@refGC-contentmethod
798569.9high performance liquid chromatography (HPLC)
3248469.9

Literature

@ref: 7985

culture collection no.: DSM 19266, KCTC 19272, JCM 16022, MSL 09

straininfo link

  • @ref: 126262
  • straininfo: 406378

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18842843Nocardioides koreensis sp. nov., Nocardioides bigeumensis sp. nov. and Nocardioides agariphilus sp. nov., isolated from soil from Bigeum Island, Korea.Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.65566-02008Actinomycetales/chemistry/*classification/*genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Genes, rRNA, Korea, Molecular Sequence Data, Peptidoglycan/chemistry, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny21046340Nocardioides ginsengisegetis sp. nov., isolated from soil of a ginseng field.Im WT, Kim SY, Liu QM, Yang JE, Lee ST, Yi TH.J Microbiol10.1007/s12275-010-0001-52010classification, isolation & purification, Soil MicrobiologyEnzymology
Phylogeny23553363Nocardioides panaciterrulae sp. nov., isolated from soil of a ginseng field, with ginsenoside converting activity.Kim JK, Liu QM, Park HY, Kang MS, Kim SC, Im WT, Yoon MHAntonie Van Leeuwenhoek10.1007/s10482-013-9919-z2013Bacterial Typing Techniques, Base Composition, Base Sequence, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Ginsenosides/*metabolism, Molecular Sequence Data, Panax/*microbiology, Phylogeny, Propionibacteriaceae/classification/genetics/*isolation & purification/*metabolism, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysis, beta-Glucosidase/metabolismMetabolism
Phylogeny26443681Nocardioides ungokensis sp. nov., isolated from lake sediment.Zhao Y, Liu Q, Kang MS, Jin F, Yu H, Im WTInt J Syst Evol Microbiol10.1099/ijsem.0.0006572015Actinomycetales/*classification/genetics/isolation & purification, Bacteria, Aerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Lakes/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryEnzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7985Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19266)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19266
19779Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM19266.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
32484Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2870428776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
126262A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer10.1093/database/baaf059StrainInfo—the central database for linked microbial strain identifiers

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