Strain identifier

BacDive ID: 11119

Type strain: Yes

Species: Nocardioides ginsengisoli

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 363868 (species)

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General

@ref: 7247

BacDive-ID: 11119

DSM-Number: 17921

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

description: Nocardioides ginsengisoli DSM 17921 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from ginseng field.

NCBI tax id

  • NCBI tax id: 363868
  • Matching level: species

strain history

@refhistory
7247<- S.-T. Lee <- W.-T. Im, KAIST; Gsoil 1124
67770W.-T. Im Gsoil 1124.
67771<- ST Lee, KAIST

doi: 10.13145/bacdive11119.20230509.8.1

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 ginsengisoli
  • full scientific name: Nocardioides ginsengisoli Cui et al. 2009

@ref: 7247

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides ginsengisoli

full scientific name: Nocardioides ginsengisoli Cui et al. 2009

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
29274positive1 µm0.3 µmrod-shapedno
67771positive

colony morphology

@refcolony colorincubation periodmedium used
19756Ivory (1014)10-14 daysISP 2
1975610-14 daysISP 5
19756Beige (1001)10-14 daysISP 6
19756Light ivory (1015)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19756noISP 2
19756noISP 5
19756noISP 6
19756noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7247R2A 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
19756ISP 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
19756ISP 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
19756ISP 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
19756ISP 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
7247TRYPTICASE 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

culture temp

@refgrowthtypetemperaturerange
7247positivegrowth28mesophilic
19756positiveoptimum28mesophilic
29274positivegrowth15-37
29274positiveoptimum30mesophilic
59563positivegrowth30-37mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
29274positivegrowth5.0-8.5alkaliphile
29274positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29274aerobe
59563aerobe
67771aerobe

spore formation

  • @ref: 29274
  • spore formation: no

halophily

  • @ref: 29274
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2927430089acetate+carbon source
2927416449alanine+carbon source
2927429016arginine+carbon source
2927422653asparagine+carbon source
2927435391aspartate+carbon source
2927427689decanoate+carbon source
2927428757fructose+carbon source
2927424265gluconate+carbon source
2927429987glutamate+carbon source
2927415428glycine+carbon source
2927427570histidine+carbon source
2927425017leucine+carbon source
2927425115malate+carbon source
2927417306maltose+carbon source
2927429864mannitol+carbon source
2927418401phenylacetate+carbon source
2927428044phenylalanine+carbon source
2927426271proline+carbon source
2927417272propionate+carbon source
2927415361pyruvate+carbon source
2927417822serine+carbon source
292749300suberic acid+carbon source
2927426986threonine+carbon source
2927416296D-tryptophan+carbon source
2927431011valerate+carbon source
2927418222xylose+carbon source
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
29274alpha-galactosidase+3.2.1.22
29274catalase+1.11.1.6
29274urease+3.5.1.5
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
19756+/-+++--+----+/-+/-+/-+/-+/-+/---

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19756+++++++--++-+-++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7247ginseng fieldPocheon ProvinceRepublic of KoreaKORAsia
59563Soil,ginseng fieldPocheonRepublic of KoreaKORAsia
67770Soil of a ginseng fieldPocheon ProvinceRepublic of KoreaKORAsia
67771From soil of the ginseng fieldPocheon provinceRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_39569.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_452;97_518;98_5991;99_39569&stattab=map
  • Last taxonomy: Nocardioides ginsengisoli subclade
  • 16S sequence: AB245396
  • Sequence Identity:
  • Total samples: 260
  • soil counts: 149
  • aquatic counts: 24
  • animal counts: 49
  • plant counts: 38

Safety information

risk assessment

  • @ref: 7247
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7247
  • description: Nocardioides ginsengisoli gene for 16S rRNA, partial sequence, strain: Gsoil 1124
  • accession: AB245396
  • length: 1447
  • database: ena
  • NCBI tax ID: 363868

GC content

@refGC-contentmethod
724770.2
6777070.2high performance liquid chromatography (HPLC)

External links

@ref: 7247

culture collection no.: DSM 17921, CCUG 52478, KCTC 19135, Gsoil 1124, JCM 16930

straininfo link

  • @ref: 80368
  • straininfo: 398531

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19643897Nocardioides ginsengisoli sp. nov., isolated from soil of a ginseng field.Cui YS, Lee ST, Im WTInt J Syst Evol Microbiol10.1099/ijs.0.010025-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, *Panax, Phylogeny, Propionibacteriaceae/*classification/genetics/*isolation & purification/metabolism, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Soil MicrobiologyMetabolism
Phylogeny26530636Nocardioides albidus sp. nov., an actinobacterium isolated from garden soil.Singh H, Du J, Trinh H, Won K, Yang JE, Yin C, Kook M, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0007302015Actinomycetales/*classification/genetics/isolation & purification, Agriculture, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny26802009Nocardioides flava sp. nov., isolated from rhizosphere of poppy plant, Republic of Korea.Singh H, Yin CSArch Microbiol10.1007/s00203-015-1178-02016Actinomycetales/*classification/genetics/isolation & purification, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/metabolism, Fatty Acids/chemistry, Papaver/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Homology, Nucleic Acid, *Soil Microbiology, Species SpecificityEnzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7247Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17921)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17921
19756Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM17921.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
29274Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2569128776041
59563Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52478)https://www.ccug.se/strain?id=52478
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
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
80368Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398531.1StrainInfo: A central database for resolving microbial strain identifiers