Strain identifier

BacDive ID: 15292

Type strain: Yes

Species: Kitasatospora herbaricolor

Strain history: KCC S-0138 <-- R. Shinobu 608.

NCBI tax ID(s): 68217 (species)

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General

@ref: 9327

BacDive-ID: 15292

DSM-Number: 40123

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

description: Kitasatospora herbaricolor DSM 40123 is a spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 68217
  • Matching level: species

strain history

@refhistory
9327<- E.B. Shirling, ISP <- R. Shinobu OEU, 608
67770KCC S-0138 <-- R. Shinobu 608.

doi: 10.13145/bacdive15292.20230509.8.1

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 herbaricolor
  • full scientific name: Kitasatospora herbaricolor (Kawato and Shinobu 1959) Labeda et al. 2017

  • synonyms

    • @ref: 20215
    • synonym: Streptomyces herbaricolor

@ref: 9327

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Kitasatospora

species: Kitasatospora herbaricolor

full scientific name: Kitasatospora herbaricolor (Kawato and Shinobu 1959) Labeda et al. 2017

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no94.42
69480100positive

Culture and growth conditions

culture medium

  • @ref: 9327
  • name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/65
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
9327positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
9327soil
67770SoilNishi Park, Fukuoka CityJapanJPNAsia

isolation source categories

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

Safety information

risk assessment

  • @ref: 9327
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces herbaricolor gene for 16S ribosomal RNA, partial sequence, strain: JCM 4138D44014120ena68217
20218Streptomyces herbaricolor gene for 16S rRNA, partial sequence, strain: NBRC 12876AB1842121468ena68217
20218Streptomyces herbaricolor gene for 16S rRNA, partial sequence, strain: NBRC 3932AB1848151451ena68217
20218Streptomyces herbaricolor strain NRRL B-3299T 16S ribosomal RNA gene, partial sequenceDQ4425051497ena68217
9327Streptomyces herbaricolor gene for 16S rRNA, partial sequence, strain: NBRC 3838AB1848011474ena68217

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kitasatospora herbaricolor JCM 4138GCA_014648975scaffoldncbi68217
66792Kitasatospora herbaricolor strain JCM 413868217.3wgspatric68217
66792Streptomyces herbaricolor DSM 401232926774088draftimg68217

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.669no
gram-positiveyes90.952no
anaerobicno99.332no
aerobicyes92.829no
halophileno92.087no
spore-formingyes93.91no
thermophileno98.919yes
glucose-utilyes90.055no
motileno93.886no
glucose-fermentno87.591no

External links

@ref: 9327

culture collection no.: DSM 40123, AS 4.1849, ATCC 23922, CBS 906.68, IFO 12876, ISP 5123, NBRC 12876, NBRC 3838, NRRL B-3299, RIA 1126, RIA 654, OEU 608, JCM 4138, BCRC 13772, CBS 424.61, CGMCC 4.1849, CGMCC 4.1887, IFO 3932, JCM 4645, NBIMCC 494, NBRC 3932, NCIMB 9837, NRRL ISP-5123, VKM Ac-793

straininfo link

  • @ref: 84386
  • straininfo: 389275

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9327Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40123)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40123
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
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/
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
84386Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389275.1StrainInfo: A central database for resolving microbial strain identifiers