Strain identifier

BacDive ID: 16345

Type strain: Yes

Species: Kitasatospora setae

Strain Designation: KM 6054

Strain history: KCC A-0304 <-- S. ?mura KM-6054.

NCBI tax ID(s): 2066 (species)

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General

@ref: 11343

BacDive-ID: 16345

DSM-Number: 43861

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

description: Kitasatospora setae KM 6054 is a spore-forming, mesophilic, Gram-positive bacterium that builds an aerial mycelium and produces antibiotic compounds.

NCBI tax id

  • NCBI tax id: 2066
  • Matching level: species

strain history

@refhistory
11343<- JCM (Kitasatosporia setae) <- KCC <- S. Omura, KM 6054 (Kitasatosporia setalba)
67770KCC A-0304 <-- S. ?mura KM-6054.

doi: 10.13145/bacdive16345.20230509.8.1

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 setae
  • full scientific name: Kitasatospora setae corrig. ?mura et al. 1983

  • synonyms

    @refsynonym
    20215Kitasatosporia setalba
    20215Kitasatosporia setae
    20215Kitasatospora setalba
    20215Streptomyces setae

@ref: 11343

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Kitasatospora

species: Kitasatospora setae

full scientific name: Kitasatospora setae ?mura et al. 1983 emend. Nouioui et al. 2018

strain designation: KM 6054

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

@refcolony colorincubation periodmedium used
19971Beige (1001)10-14 daysISP 2
19971Beige (1001)10-14 daysISP 3
19971Beige (1001)10-14 daysISP 4
19971Beige (1001)10-14 daysISP 5
19971Beige (1001)10-14 daysISP 6
19971Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19971yesAerial MyceliumGreyISP 2
19971noISP 3
19971yesAerial MyceliumWhiteISP 4
19971yesAerial MyceliumWhiteISP 5
19971yesAerial MyceliumWhiteISP 6
19971yesAerial MyceliumWhiteISP 7

multimedia

@refmultimedia contentintellectual property rightscaption
11343https://www.dsmz.de/microorganisms/photos/DSM_43861-1.jpg© Leibniz-Institut DSMZ
11343https://www.dsmz.de/microorganisms/photos/DSM_43861-2.jpg© Leibniz-Institut DSMZ
11343https://www.dsmz.de/microorganisms/photos/DSM_43861.jpg© Leibniz-Institut DSMZMedium 65 28°C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11343GYM 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
19971ISP 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
19971ISP 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:
19971ISP 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
19971ISP 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
19971ISP 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
19971ISP 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
11343ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf

culture temp

@refgrowthtypetemperaturerange
11343positivegrowth28mesophilic
19971positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore descriptionspore formationconfidence
19971Formation of spore chains (rectiflixibilis), spore surface smoothyes
69481yes100
69480yes100

compound production

@refcompound
11343setamycine
20216Setamycine
19971Propioxanthin
19971Bafilomycin B

observation

  • @ref: 67770
  • observation: quinones: MK-9(H6), MK-9(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1997162968cellulose-
1997116634raffinose-
1997126546rhamnose-
1997128757fructose-
1997129864mannitol-
1997117268myo-inositol-
1997118222xylose-
1997117992sucrose-
1997122599arabinose+
1997117234glucose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refmetaboliteproductionChebi-ID
67770setamycinyes
68368acetoinno15688
68368indoleno35581
68368hydrogen sulfideno16136

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
19971+---+-----+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11343soilTokyo, Setagaya-kuJapanJPNAsia
67770SoilSetagaya-ku, TokyoJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5928.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_148;97_159;98_3799;99_5928&stattab=map
  • Last taxonomy: Kitasatospora setae
  • 16S sequence: U93332
  • Sequence Identity:
  • Total samples: 223
  • soil counts: 163
  • aquatic counts: 8
  • animal counts: 16
  • plant counts: 36

Safety information

risk assessment

  • @ref: 11343
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218K.setae 16S ribosomal RNA genes, partial cdsM552201464ena2066
20218Kitasatosporia setalba 16S ribosomal RNA gene, partial sequenceU933321482ena452652
20218Kitasatosporia setalba 16S-23S ribosomal RNA gene spacer, partial sequenceU93333277ena452652
20218Kitasatospora setae gene for 16S ribosomal RNAAB0228681523ena452652
20218Kitasatospora setae gene for 16S rRNA, partial sequence, strain: NBRC 14216AB1845761479ena452652

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kitasatospora setae KM-6054452652.3completepatric452652
66792Kitasatospora setae KM-6054, NBRC 142162511231086completeimg452652
67770Kitasatospora setae KM-6054GCA_000269985completencbi452652
67770Kitasatospora setae NRRL B-16185GCA_000716965contigncbi2066

GC content

@refGC-contentmethod
6777074.2genome sequence analysis
6777072.5thermal denaturation, midpoint method (Tm)
6777073.1high performance liquid chromatography (HPLC)
6777074.1genome sequence analysis
6777073.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes94.174no
anaerobicno99.469no
halophileno93.19no
spore-formingyes94.844yes
glucose-utilyes88.744yes
aerobicyes90.635no
flagellatedno97.892no
thermophileno98.182yes
motileno94.352no
glucose-fermentno90.177no

External links

@ref: 11343

culture collection no.: DSM 43861, ATCC 33774, IFO 14216, JCM 3304, KCC A-0304, NBRC 14216, BCRC 13404, CGMCC 4.1210, CGMCC 4.1226, CGMCC 4.1247, HUT 6571, IMSNU 21321, KACC 20032, KCTC 9182, KCTC 9793, NCIMB 13310, NRRL B-16185, PCM 2323, VKM Ac-900

straininfo link

  • @ref: 85400
  • straininfo: 319088

literature

topicPubmed-IDtitleauthorsjournalyearmeshDOItopic2
Phylogeny11189356[Taxonomic studies of two Streptomycete strains AS 4.693 and AS 4.702].Liu Z, Qian Y, Zhang Y, Shi Y, Xie JWei Sheng Wu Xue Bao1997DNA, Bacterial/genetics, Streptomyces/*classification/genetics, Terminology as Topic
Genetics21059706Genome sequence of Kitasatospora setae NBRC 14216T: an evolutionary snapshot of the family Streptomycetaceae.Ichikawa N, Oguchi A, Ikeda H, Ishikawa J, Kitani S, Watanabe Y, Nakamura S, Katano Y, Kishi E, Sasagawa M, Ankai A, Fukui S, Hashimoto Y, Kamata S, Otoguro M, Tanikawa S, Nihira T, Horinouchi S, Ohnishi Y, Hayakawa M, Kuzuyama T, Arisawa A, Nomoto F, Miura H, Takahashi Y, Fujita NDNA Res2010Amino Acid Sequence, Antitrichomonal Agents/metabolism, Base Sequence, Chromosomes, Bacterial/genetics, DNA, Bacterial/analysis, *Evolution, Molecular, Gene Expression Regulation, Developmental, *Genome, Bacterial, Macrolides/metabolism, Molecular Sequence Data, Phylogeny, RNA, Bacterial/analysis, RNA, Ribosomal, 16S/analysis, RNA, Transfer/genetics, Streptomycetaceae/*classification/*genetics10.1093/dnares/dsq026Phylogeny
22561881Kitasetaline, a novel beta-carboline alkaloid from Kitasatospora setae NBRC 14216T.Aroonsri A, Kitani S, Ikeda H, Nihira TJ Biosci Bioeng2012Animals, Carbolines/*chemistry, Chromatography, High Pressure Liquid, Genes, Bacterial/genetics, Streptomycetaceae/*chemistry/*genetics10.1016/j.jbiosc.2012.02.027

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11343Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43861)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43861
19971Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43861.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
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/
68368Automatically annotated from API 20E
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
85400Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID319088.1StrainInfo: A central database for resolving microbial strain identifiers