Strain identifier

BacDive ID: 15498

Type strain: Yes

Species: Kitasatospora purpeofusca

Strain Designation: H-5080

Strain history: KCC S-0156 <-- G. Nakamura <-- H. Yonehara (IAM 0073) <-- T. Yamaguchi H-5080.

NCBI tax ID(s): 67352 (species)

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General

@ref: 9434

BacDive-ID: 15498

DSM-Number: 40283

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

description: Kitasatospora purpeofusca H-5080 is a spore-forming, mesophilic, Gram-positive bacterium that produces antibiotic compounds and was isolated from soil.

NCBI tax id

  • NCBI tax id: 67352
  • Matching level: species

strain history

@refhistory
9434<- E.B. Shirling, ISP <- T. Yamaguchi, H-5080
67770KCC S-0156 <-- G. Nakamura <-- H. Yonehara (IAM 0073) <-- T. Yamaguchi H-5080.

doi: 10.13145/bacdive15498.20230509.8.1

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 purpeofusca
  • full scientific name: Kitasatospora purpeofusca (Yamaguchi and Saburi 1955) Labeda et al. 2017

  • synonyms

    • @ref: 20215
    • synonym: Streptomyces purpeofuscus

@ref: 9434

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Kitasatospora

species: Kitasatospora purpeofusca

full scientific name: Kitasatospora purpeofusca (Yamaguchi and Saburi 1955) Labeda et al. 2017

strain designation: H-5080

type strain: yes

Morphology

cell morphology

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

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9434GYM 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
9434ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf

culture temp

@refgrowthtypetemperaturerange
18579positiveoptimum28mesophilic
9434positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

@refcompound
9434negamycin
9434anti-trichomonas antibiotic
20216Nagemycin

halophily

  • @ref: 18579
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1857917234glucose+
1857922599arabinose-
1857917992sucrose-
1857918222xylose-
1857917268myo-inositol-
1857929864mannitol-
1857928757fructose-
1857926546rhamnose-
1857916634raffinose-
1857962968cellulose-
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
18579------+--+-

Isolation, sampling and environmental information

isolation

  • @ref: 9434
  • sample type: soil
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1375.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_148;97_159;98_177;99_1375&stattab=map
  • Last taxonomy: Kitasatospora
  • 16S sequence: AJ781364
  • Sequence Identity:
  • Total samples: 1391
  • soil counts: 1166
  • aquatic counts: 19
  • animal counts: 107
  • plant counts: 99

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
185791German classification
94341Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces purpeofuscus gene for 16S rRNA, partial sequenceAB122757564ena67352
20218Streptomyces purpeofuscus strain IFO 12905 16S ribosomal RNA gene, partial sequenceAY9998631420ena67352
20218Streptomyces purpeofuscus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4665D44294121ena67352
20218Streptomyces purpeofuscus gene for 16S rRNA, partial sequence, strain: NBRC 12905AB1842341451ena67352
9434Streptomyces purpeofuscus 16S rRNA gene, type strain LMG 20283AJ7813641476ena67352

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
67770Kitasatospora purpeofusca NRRL ISP-5283GCA_000716225scaffoldncbi67352
67770Kitasatospora purpeofusca NRRL B-1817GCA_000718025contigncbi67352

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes78.585no
gram-positiveyes91.529no
anaerobicno99.064no
aerobicyes91.451no
halophileno94.75no
spore-formingno83.19no
glucose-utilyes85.087no
flagellatedno91.307no
thermophileno98.705yes
glucose-fermentno66.54no

External links

@ref: 9434

culture collection no.: DSM 40283, ATCC 23952, CBS 935.68, IFO 12905, ISP 5283, KCC S-0156, KCC S-0509, NBRC 12905, NRRL B-1817, RIA 1197, JCM 4156, BCRC 12093, CGMCC 4.1767, CGMCC 4.1999, JCM 4665, KCTC 19967, NCIMB 9822, NRRL ISP-5283

straininfo link

  • @ref: 84584
  • straininfo: 264282

literature

  • topic: Phylogeny
  • Pubmed-ID: 32924916
  • title: Kitasatospora acidiphila sp. nov., isolated from pine grove soil, exhibiting antimicrobial potential.
  • authors: Kim MJ, Roh SG, Kim MK, Park C, Kim S, Kim SB
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.004450
  • year: 2020
  • mesh: Bacterial 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/chemistry
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9434Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40283)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40283
18579Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40283.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
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
84584Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID264282.1StrainInfo: A central database for resolving microbial strain identifiers