Strain identifier

BacDive ID: 11113

Type strain: Yes

Species: Nocardioides kribbensis

Strain Designation: KSL-2

Strain history: CIP <- 2005, KCTC <- I.G. Kim, KRIBB: strain KSL-2

NCBI tax ID(s): 305517 (species)

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General

@ref: 6360

BacDive-ID: 11113

DSM-Number: 16314

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

description: Nocardioides kribbensis KSL-2 is an aerobe, spore-forming, mesophilic bacterium that was isolated from Soil.

NCBI tax id

  • NCBI tax id: 305517
  • Matching level: species

strain history

@refhistory
6360<- J.-H. Yoon <- In-Gi Kim, KSL-2
400532005, KCTC
67770KCTC 19038 <-- I.-G. Kim KSL-2.
67771<- IG Kim, KRIBB
120498CIP <- 2005, KCTC <- I.G. Kim, KRIBB: strain KSL-2

doi: 10.13145/bacdive11113.20230509.8.1

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 kribbensis
  • full scientific name: Nocardioides kribbensis Yoon et al. 2005

@ref: 6360

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides kribbensis

full scientific name: Nocardioides kribbensis Yoon et al. 2005

strain designation: KSL-2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31469positive1.75 µm0.9 µmrod-shapedno
67771positive
120498positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18608Corn yellow (1006)10-14 daysISP 2
18608Golden yellow (1004)10-14 daysISP 3
18608Golden yellow (1004)10-14 daysISP 4
18608Golden yellow (1004)10-14 daysISP 5
18608Golden yellow (1004)10-14 daysISP 6
18608Sand yellow (1002)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18608noISP 2
18608noISP 3
18608noISP 4
18608noISP 5
18608noISP 6
18608noISP 7

pigmentation

  • @ref: 31469
  • production: no

multimedia

  • @ref: 6360
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_16314.jpg
  • caption: Medium 830 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6360R2A 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
18608ISP 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
18608ISP 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:
18608ISP 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
18608ISP 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
18608ISP 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
18608ISP 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
40053MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
6360TRYPTICASE 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
120498CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
6360positivegrowth28mesophilic
18608positiveoptimum28mesophilic
31469positivegrowth04-35
31469positiveoptimum30mesophilic
40053positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31469positivegrowth06-11alkaliphile
31469positiveoptimum9

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31469aerobe
67771aerobe
120498obligate aerobe

spore formation

  • @ref: 31469
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
31469NaClpositivegrowth<3.0 %
31469NaClpositiveoptimum1.5 %

murein

  • @ref: 6360
  • murein short key: A41.01
  • type: A3gamma LL-Dpm-Gly

observation

@refobservation
31469aggregates in clumps
67770quinones: MK-8(H4)
67771quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1860862968cellulose+
1860816634raffinose+/-
1860826546rhamnose+
1860828757fructose+
1860829864mannitol+
1860817268myo-inositol+/-
1860818222xylose-
1860817992sucrose+
1860822599arabinose-
1860817234glucose+
3146917057cellobiose+carbon source
3146928260galactose+carbon source
314695291gelatin+carbon source
3146917234glucose+carbon source
3146917306maltose+carbon source
3146929864mannitol+carbon source
3146916634raffinose+carbon source
3146926546rhamnose+carbon source
3146933942ribose+carbon source
3146930911sorbitol+carbon source
3146917992sucrose+carbon source
3146927082trehalose+carbon source
3146953424tween 20+carbon source
3146953423tween 40+carbon source
3146953425tween 60+carbon source
3146953426tween 80+carbon source
314694853esculin+hydrolysis
3146917632nitrate+reduction
12049817632nitrate-reduction
12049816301nitrite-reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
6837917992sucrose+fermentation

metabolite production

  • @ref: 120498
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31469cytochrome oxidase+1.9.3.1
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
68379pyrazinamidase-3.5.1.B15
120498oxidase+
120498alcohol dehydrogenase-1.1.1.1
120498catalase+1.11.1.6
120498lysine decarboxylase-4.1.1.18
120498ornithine decarboxylase-4.1.1.17
120498urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
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

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
18608-+/-+/--++-+-+/-+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18608+++++-++++--++++---
120498+++-+--+++++--++----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
6360SoilRepublic of KoreaKORAsia
67770Alkaline soilRepublic of KoreaKORAsia
67771From alkaline soilRepublic of KoreaKORAsia
120498Environment, Alkaline soilRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4167.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_2111;97_2543;98_3147;99_4167&stattab=map
  • Last taxonomy: Nocardioides kribbensis subclade
  • 16S sequence: AY835924
  • Sequence Identity:
  • Total samples: 2145
  • soil counts: 706
  • aquatic counts: 463
  • animal counts: 685
  • plant counts: 291

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
63601Risk group (German classification)
186081Hazard group
1204981Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6360
  • description: Nocardioides kribbensis strain KSL-2 16S ribosomal RNA gene, partial sequence
  • accession: AY835924
  • length: 1476
  • database: ena
  • NCBI tax ID: 305517

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides kribbensis DSM 16314GCA_015070375contigncbi305517
66792Nocardioides kribbensis strain DSM 16314305517.3wgspatric305517

GC content

@refGC-contentmethod
636073
3146974
6777073high performance liquid chromatography (HPLC)
6777173.0high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes93.802yes
anaerobicno97.933yes
halophileno91.108no
spore-formingno74.352no
glucose-utilyes88.533yes
motileno79.213yes
aerobicyes93.995yes
flagellatedno91.791no
thermophileno98.531no
glucose-fermentno89.962no

External links

@ref: 6360

culture collection no.: DSM 16314, KCTC 19038, JCM 13594, CIP 108882

straininfo link

  • @ref: 80362
  • straininfo: 232299

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16014490Nocardioides kribbensis sp. nov., isolated from an alkaline soil.Yoon JH, Kim IG, Lee MH, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.63631-02005Actinomycetales/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny18071922Nocardioides islandiensis sp. nov., isolated from soil in Bigeum Island Korea.Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJAntonie Van Leeuwenhoek10.1007/s10482-007-9217-82007Actinomycetales/classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny18191931Nocardioides halotolerans sp. nov., isolated from soil on Bigeum Island, Korea.Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJSyst Appl Microbiol10.1016/j.syapm.2007.10.0032008Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Aerobiosis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Korea, Microscopy, Electron, Scanning, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, *Soil Microbiology, Vitamin K 2/analysisMetabolism
Phylogeny19126721Nocardioides basaltis sp. nov., isolated from black beach sand.Kim KH, Roh SW, Chang HW, Nam YD, Yoon JH, Jeon CO, Oh HM, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.65785-02009Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Korea, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, *Silicon Dioxide, Species SpecificityPhenotype
Phylogeny22345140Nocardioides szechwanensis sp. nov. and Nocardioides psychrotolerans sp. nov., isolated from a glacier.Liu Q, Xin YH, Liu HC, Zhou YG, Wen YInt J Syst Evol Microbiol10.1099/ijs.0.038091-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Ice Cover/*microbiology, Molecular Sequence Data, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/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
Phylogeny24844261Nocardioides nanhaiensis sp. nov., an actinobacterium isolated from a marine sediment sample.Zhang DF, Zhong JM, Zhang XM, Jiang Z, Zhou EM, Tian XP, Zhang S, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.062851-02014Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6360Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16314)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16314
18608Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM16314.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
31469Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2776928776041
40053Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6561
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/
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
80362Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232299.1StrainInfo: A central database for resolving microbial strain identifiers
120498Curators of the CIPCollection of Institut Pasteur (CIP 108882)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108882