Strain identifier

BacDive ID: 14862

Type strain: Yes

Species: Kitasatospora nipponensis

Strain Designation: 2148-013

Strain history: I. Groth 2148-013 (=HKI 0315) <-- Ch. Weigel.

NCBI tax ID(s): 258049 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 12091

BacDive-ID: 14862

DSM-Number: 44787

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

description: Kitasatospora nipponensis 2148-013 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 258049
  • Matching level: species

strain history

@refhistory
12091<- I. Groth, HKI, 07745 Jena, Germany; 2148-013 <- Ch. Weigel
67770I. Groth 2148-013 (=HKI 0315) <-- Ch. Weigel.

doi: 10.13145/bacdive14862.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Kitasatosporales
  • family: Streptomycetaceae
  • genus: Kitasatospora
  • species: Kitasatospora nipponensis
  • full scientific name: Kitasatospora nipponensis Groth et al. 2004

@ref: 12091

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Kitasatospora

species: Kitasatospora nipponensis

full scientific name: Kitasatospora nipponensis Groth et al. 2004

strain designation: 2148-013

type strain: yes

Morphology

cell morphology

  • @ref: 31218
  • gram stain: positive
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
20117Brown beige (1011)10-14 daysISP 2
20117Brown beige (1011)10-14 daysISP 3
20117Brown beige (1011)10-14 daysISP 4
20117Beige (1001)10-14 daysISP 5
20117Beige (1001)10-14 daysISP 6
20117Brown beige (1011)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20117yesAerial MyceliumWhiteISP 2
20117yesAerial MyceliumSquirrel greyISP 3
20117yesAerial MyceliumSquirrel greyISP 4
20117noISP 5
20117noISP 6
20117noISP 7

pigmentation

  • @ref: 31218
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12091GYM 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
20117ISP 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
20117ISP 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:
20117ISP 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
20117ISP 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
20117ISP 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
20117ISP 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
12091ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://mediadive.dsmz.de/medium/84Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
12091STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)yeshttps://mediadive.dsmz.de/medium/252Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
12091positivegrowth28mesophilic
20117positiveoptimum28mesophilic
31218positivegrowth10-32
31218positiveoptimum26.5mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
31218positivegrowth05-08
31218positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

  • @ref: 31218
  • oxygen tolerance: aerobe

spore formation

  • @ref: 31218
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
31218NaClpositivegrowth0-2.5 %
31218NaClpositiveoptimum1.25 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2011717234glucose+
2011722599arabinose-
2011717992sucrose+/-
2011718222xylose+/-
2011717268myo-inositol-
2011729864mannitol-
2011728757fructose+
2011726546rhamnose-
2011716634raffinose+/-
2011762968cellulose+/-
3121828757fructose+carbon source
3121817234glucose+carbon source
3121817992sucrose+carbon source

metabolite production

  • @ref: 31218
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
31218acid phosphatase+3.1.3.2
31218alkaline phosphatase+3.1.3.1
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
20117-++-+----+----+-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12091soilKumaguraJapanJPNAsia
67770SoilKumaguraJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_109284.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_148;97_159;98_177;99_109284&stattab=map
  • Last taxonomy: Kitasatospora
  • 16S sequence: AY442263
  • Sequence Identity:
  • Total samples: 15
  • soil counts: 15

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
120911Risk group (German classification)
201171German classification

Sequence information

16S sequences

  • @ref: 12091
  • description: Kitasatospora nipponensis strain HKI 0315 16S ribosomal RNA gene, partial sequence
  • accession: AY442263
  • length: 1390
  • database: ena
  • NCBI tax ID: 258049

External links

@ref: 12091

culture collection no.: DSM 44787, HKI 0315, NCIMB 13975, JCM 13004, IAM 15272, NBRC 101836

straininfo link

  • @ref: 83975
  • straininfo: 134433

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15545445Five novel Kitasatospora species from soil: Kitasatospora arboriphila sp. nov., K. gansuensis sp. nov., K. nipponensis sp. nov., K. paranensis sp. nov. and K. terrestris sp. nov.Groth I, Rodriguez C, Schutze B, Schmitz P, Leistner E, Goodfellow MInt J Syst Evol Microbiol10.1099/ijs.0.63070-02004Anti-Bacterial Agents/pharmacology, Bacterial Typing Techniques, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, rRNA/genetics, Hydrogen-Ion Concentration, Japan, Microscopy, Electron, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Saline Solution, Hypertonic, Sequence Analysis, DNA, *Soil Microbiology, Streptomycetaceae/*classification/cytology/*isolation & purification/physiology, TemperatureEnzymology
Phylogeny32924916Kitasatospora acidiphila sp. nov., isolated from pine grove soil, exhibiting antimicrobial potential.Kim MJ, Roh SG, Kim MK, Park C, Kim S, Kim SBInt J Syst Evol Microbiol10.1099/ijsem.0.0044502020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Forests, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Pinus/*microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Streptomycetaceae/*classification/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12091Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44787)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44787
20117Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44787.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
31218Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2754428776041
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
83975Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134433.1StrainInfo: A central database for resolving microbial strain identifiers