Strain identifier

BacDive ID: 14858

Type strain: Yes

Species: Kitasatospora cineracea

Strain Designation: SK-3255

Strain history: CIP <- 2001, JCM <- S. Omura, Japan: strain SK-3255

NCBI tax ID(s): 88074 (species)

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General

@ref: 12085

BacDive-ID: 14858

DSM-Number: 44780

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

description: Kitasatospora cineracea SK-3255 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 88074
  • Matching level: species

strain history

@refhistory
12085<- JCM <- S. Omura; SK-3255
67770S. ?mura SK-3255.
118285CIP <- 2001, JCM <- S. Omura, Japan: strain SK-3255

doi: 10.13145/bacdive14858.20230509.8.1

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 cineracea
  • full scientific name: Kitasatospora cineracea Tajima et al. 2001

@ref: 12085

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Kitasatospora

species: Kitasatospora cineracea

full scientific name: Kitasatospora cineracea Tajima et al. 2001

strain designation: SK-3255

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.024
69480100positive
118285nopositiverod-shaped

colony morphology

  • @ref: 118285
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12085STARCH - 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
12085GYM 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
40702MEDIUM 275 - for Actinomadura rugatobispora and Actinomadura verrucososporayesDistilled water make up to (1000.000 ml);Sodium chloride (1.000 g);Magnesium sulphate heptahydrate (1.000 g);Agar (20.000 g);Ammonium sulphate (2.000 g);Starch maize (10.000 g);Calcium carbonate (2.000 g);Trace salt solution - M00447 (1.000 ml)
12085ROLLED 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
118285CIP Medium 275yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=275

culture temp

@refgrowthtypetemperaturerange
12085positivegrowth28mesophilic
40702positivegrowth30mesophilic
67770positivegrowth28mesophilic
118285positivegrowth25-37mesophilic
118285nogrowth10psychrophilic
118285nogrowth41thermophilic
118285nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118285
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

  • @ref: 118285
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate+builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose+builds acid from28066
68371xylitol-builds acid from17151
68371glycogen+builds acid from28087
68371starch+builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose+builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose+builds acid from17634
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
118285esculin+hydrolysis4853
118285hippurate-hydrolysis606565
118285nitrate-reduction17632
118285nitrite-reduction16301
118285nitrate-respiration17632

antibiotic resistance

  • @ref: 118285
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 118285
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11828515688acetoin-
11828517234glucose-

enzymes

@refvalueactivityec
118285oxidase-
118285beta-galactosidase-3.2.1.23
118285alcohol dehydrogenase-1.1.1.1
118285gelatinase+/-
118285amylase-
118285DNase-
118285caseinase-3.4.21.50
118285catalase+1.11.1.6
118285tween esterase+
118285gamma-glutamyltransferase-2.3.2.2
118285lecithinase+
118285lipase-
118285lysine decarboxylase-4.1.1.18
118285ornithine decarboxylase-4.1.1.17
118285phenylalanine ammonia-lyase-4.3.1.24
118285protease+
118285tryptophan deaminase-
118285urease+3.5.1.5
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

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118285--++++----++-+-+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118285---+++---+/-+---------------+--------++-+-------+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118285+-+-+----+++---++-++++---------+-----------------++--+-----++-+--++-----+--+--+++-----+-++++-+-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12085soilTokyoJapanJPNAsia
67770SoilNishigahara, Kita-ku, TokyoJapanJPNAsia
118285Environment, SoilNishigahara, TokyoJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_12635.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_148;97_159;98_2879;99_12635&stattab=map
  • Last taxonomy: Kitasatospora
  • 16S sequence: AB022875
  • Sequence Identity:
  • Total samples: 19
  • soil counts: 15
  • aquatic counts: 3
  • animal counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
120851Risk group (German classification)
1182851Risk group (French classification)

Sequence information

16S sequences

  • @ref: 12085
  • description: Kitasatospora cineracea gene for 16S ribosomal RNA, strain: SK-3255
  • accession: AB022875
  • length: 1515
  • database: ena
  • NCBI tax ID: 88074

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kitasatospora cineracea strain DSM 4478088074.3wgspatric88074
66792Kitasatospora cineracea DSM 447802781126035draftimg88074
67770Kitasatospora cineracea DSM 44780GCA_003751605contigncbi88074

GC content

@refGC-contentmethod
1208573.7
6777073.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno94.11no
flagellatedno98.403no
gram-positiveyes93.487no
anaerobicno99.534no
halophileno94.059no
spore-formingyes92.76no
thermophileno98.597no
glucose-utilyes88.415no
aerobicyes93.699no
glucose-fermentno90.355no

External links

@ref: 12085

culture collection no.: DSM 44780, CIP 107255, IFO 16452, JCM 10915, KCTC 19932, NBRC 16452, NRRL B-23134, BCRC 16811, IAM 15157, NCIMB 14261, NRRL B-24134

straininfo link

  • @ref: 83971
  • straininfo: 100706

literature

  • topic: Phylogeny
  • Pubmed-ID: 11594607
  • title: Description of two novel species of the genus Kitasatospora Omura et al. 1982, Kitasatospora cineracea sp. nov. and Kitasatospora niigatensis sp. nov.
  • authors: Tajima K, Takahashi Y, Seino A, Iwai Y, Omura S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-51-5-1765
  • year: 2001
  • mesh: Cell Wall/chemistry, DNA, Ribosomal/analysis, Diaminopimelic Acid/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/*genetics, *Sequence Analysis, DNA, *Soil Microbiology, Streptomycetaceae/*classification/genetics/*isolation & purification/physiology/ultrastructure
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
12085Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44780)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44780
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
40702Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4670
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/
68371Automatically annotated from API 50CH acid
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
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
83971Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100706.1StrainInfo: A central database for resolving microbial strain identifiers
118285Curators of the CIPCollection of Institut Pasteur (CIP 107255)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107255