Strain identifier

BacDive ID: 14859

Type strain: Yes

Species: Kitasatospora niigatensis

Strain Designation: SK-3406

Strain history: CIP <- 2001, JCM <- S. Omura, Japan: strain SK-3406

NCBI tax ID(s): 88075 (species)

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General

@ref: 12086

BacDive-ID: 14859

DSM-Number: 44781

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

description: Kitasatospora niigatensis SK-3406 is a facultative anaerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 88075
  • Matching level: species

strain history

@refhistory
12086<- JCM <- S. Omura; SK-3406
67770S. ?mura SK-3406.
121301CIP <- 2001, JCM <- S. Omura, Japan: strain SK-3406

doi: 10.13145/bacdive14859.20230509.8.1

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

@ref: 12086

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Kitasatospora

species: Kitasatospora niigatensis

full scientific name: Kitasatospora niigatensis Tajima et al. 2001

strain designation: SK-3406

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.304
69480100positive
121301nopositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12086GYM 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
32861MEDIUM 366 - for Actinoalloteichus cyanogriseusyesDistilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)
12086ROLLED 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
12086STARCH - 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
121301CIP Medium 366yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=366

culture temp

@refgrowthtypetemperaturerange
12086positivegrowth28mesophilic
32861positivegrowth30mesophilic
67770positivegrowth28mesophilic
121301positivegrowth30-37mesophilic
121301nogrowth10psychrophilic
121301nogrowth25mesophilic
121301nogrowth41thermophilic
121301nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121301
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
121301NaClpositivegrowth0-4 %
121301NaClnogrowth6 %
121301NaClnogrowth8 %
121301NaClnogrowth10 %

observation

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
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-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
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
121301citrate-carbon source16947
121301esculin-hydrolysis4853
121301hippurate-hydrolysis606565
121301nitrate+reduction17632
121301nitrite-reduction16301
121301nitrate+respiration17632

metabolite production

  • @ref: 121301
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12130115688acetoin+
12130117234glucose+

enzymes

@refvalueactivityec
121301oxidase-
121301beta-galactosidase+3.2.1.23
121301alcohol dehydrogenase-1.1.1.1
121301gelatinase-
121301amylase-
121301DNase-
121301caseinase-3.4.21.50
121301catalase-1.11.1.6
121301tween esterase+
121301gamma-glutamyltransferase-2.3.2.2
121301lecithinase-
121301lipase-
121301lysine decarboxylase+4.1.1.18
121301ornithine decarboxylase+4.1.1.17
121301phenylalanine ammonia-lyase-4.3.1.24
121301tryptophan deaminase-
121301urease-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
121301-+--------++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121301+/---------+/-+/--------+/----------------------------+/--+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121301+++++--+-------+----------------------------------------------+--+--------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12086soilNiigata CityJapanJPNAsia
67770SoilNiigata CityJapanJPNAsia
121301Environment, SoilNiigataJapanJPNAsia

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: AB249960
  • Sequence Identity:
  • Total samples: 19
  • soil counts: 15
  • aquatic counts: 3
  • animal counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
120861Risk group (German classification)
1213011Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Kitasatospora niigatensis gene for 16S rRNA, partial sequence, strain: NBRC 16453AB2499601473ena88075
12086Kitasatospora niigatensis gene for 16S ribosomal RNA, strain: SK-3406AB0228761516ena88075

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kitasatospora niigatensis strain DSM 4478188075.4wgspatric88075
66792Kitasatospora niigatensis DSM 447812786546131draftimg88075
67770Kitasatospora niigatensis DSM 44781GCA_003814885contigncbi88075

GC content

@refGC-contentmethod
1208673.5
6777073.5high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.954no
flagellatedno98.134no
gram-positiveyes93.759no
anaerobicno99.515no
halophileno94.092no
spore-formingyes94.033no
thermophileno98.728yes
glucose-utilyes88.836no
aerobicyes93.462no
glucose-fermentno90.358no

External links

@ref: 12086

culture collection no.: DSM 44781, CIP 107256, IFO 16453, JCM 10916, KCTC 19933, NBRC 16453, NRRL B-24135, BCRC 16812, IAM 15156

straininfo link

  • @ref: 83972
  • straininfo: 100707

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/urltitlejournalpubmed
12086Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44781)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44781
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
32861Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4671
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
83972Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100707.1StrainInfo: A central database for resolving microbial strain identifiers
121301Curators of the CIPCollection of Institut Pasteur (CIP 107256)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107256