Strain identifier

BacDive ID: 15413

Type strain: Yes

Species: Kitasatospora misakiensis

Strain Designation: IPCR 7617

Strain history: KCC S-0062 <-- G. Nakamura 7617 (=1755).

NCBI tax ID(s): 67330 (species)

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General

@ref: 9279

BacDive-ID: 15413

DSM-Number: 40222

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, antibiotic compound production

description: Kitasatospora misakiensis IPCR 7617 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and produces antibiotic compounds.

NCBI tax id

  • NCBI tax id: 67330
  • Matching level: species

strain history

@refhistory
9279<- E.B. Shirling, ISP <- S. Suzuki, IPCR, 7617
67770KCC S-0062 <-- G. Nakamura 7617 (=1755).

doi: 10.13145/bacdive15413.20230509.8.1

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 misakiensis
  • full scientific name: Kitasatospora misakiensis (Nakamura 1961) Labeda et al. 2017

  • synonyms

    • @ref: 20215
    • synonym: Streptomyces misakiensis

@ref: 9279

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Kitasatospora

species: Kitasatospora misakiensis

full scientific name: Kitasatospora misakiensis (Nakamura 1961) Labeda et al. 2017

strain designation: IPCR 7617

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
19425Light red10-14 daysISP 2
19425Yellow red10-14 daysISP 3
19425Yellow10-14 daysISP 4
19425Brown10-14 daysISP 5
19425Brown10-14 daysISP 6
19425Brown red10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19425yesAerial MyceliumGreyISP 2
19425yesAerial MyceliumLight greyISP 3
19425yesAerial MyceliumGreyISP 4
19425yesAerial MyceliumGreyISP 5
19425noISP 6
19425yesAerial MyceliumGreyISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9279GYM 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
19425ISP 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
19425ISP 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:
19425ISP 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
19425ISP 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
19425ISP 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
19425ISP 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
9279ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf

culture temp

@refgrowthtypetemperaturerange
19425positiveoptimum28mesophilic
9279positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 19425
  • spore description: Formation of spore chains: rectiflixibilis, spore surface: smooth
  • spore formation: yes

compound production

@refcompound
9279tubermycin A
9279tubermycin B
9279tubermycin A, B
20216Tubermycin A
20216Tubermycin B
67770Tubermycins A and B

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1942562968cellulose-
1942516634raffinose-
1942526546rhamnose-
1942528757fructose+
1942529864mannitol-
1942517268myo-inositol-
1942518222xylose-
1942517992sucrose+
1942522599arabinose-
1942517234glucose+
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19425+++++-+--+-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
9279soilJapanJPNAsia
67770SoilJapanJPNAsiaMisaki, Kanagawa Pref.

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
92791Risk group (German classification)
194251Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces misakiensis strain DSM 40222 16S ribosomal RNA gene, partial sequenceAY9998391420ena67330
20218Streptomyces misakiensis gene for 16S rRNA, partial sequenceAB122749564ena67330
20218Streptomyces misakiensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 4653D44287120ena67330
20218Streptomyces misakiensis 16S rRNA gene, type strain LMG 19369AJ7813251476ena67330
20218Streptomyces misakiensis gene for 16S rRNA, partial sequence, strain: NBRC 12891AB1842231473ena67330
9279Streptomyces misakiensis gene for 16S rRNA, partial sequence, strain:IFO 12891AB2176051473ena67330

Genome sequences

  • @ref: 67770
  • description: Kitasatospora misakiensis NRRL B-2923
  • accession: GCA_000715585
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 67330

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno94.306no
flagellatedno98.17no
gram-positiveyes92.759no
anaerobicno99.58no
halophileno93.452no
spore-formingyes94.921yes
thermophileno98.812yes
glucose-utilyes91.809no
aerobicyes92.626no
glucose-fermentno91.469no

External links

@ref: 9279

culture collection no.: DSM 40222, ATCC 23938, CBS 278.65, CBS 922.68, IFO 12891, ISP 5222, JCM 4062, JCM 4653, NBRC 12891, NRRL B-2923, RIA 1166, BCRC 13799, CGMCC 4.1437, IFM 1195, KCTC 19951, NCIMB 9852, NRRL ISP-5222, VKM Ac-625

straininfo link

  • @ref: 84502
  • straininfo: 14119

literature

  • topic: Phylogeny
  • Pubmed-ID: 26790410
  • title: Streptomyces polygonati sp. nov., an endophytic actinomycete isolated from a root of Polygonatum odoratum (Mill.).
  • authors: Guo S, Liu C, Liu S, Guan X, Guo L, Jia F, Wang X, Xiang W
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000906
  • year: 2016

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9279Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40222)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40222
19425Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40222.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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
84502Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14119.1StrainInfo: A central database for resolving microbial strain identifiers