Strain identifier

BacDive ID: 6325

Type strain: Yes

Species: Kineosporia mikuniensis

Strain Designation: I-463

Strain history: CIP <- 1998, JCM <- T. Itoh: strain I-463

NCBI tax ID(s): 1307457 (strain), 499547 (species)

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General

@ref: 11511

BacDive-ID: 6325

DSM-Number: 44390

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

description: Kineosporia mikuniensis I-463 is a spore-forming, mesophilic, Gram-negative bacterium that was isolated from sphagnum.

NCBI tax id

NCBI tax idMatching level
1307457strain
499547species

strain history

@refhistory
11511<- JCM <- T. Itoh; I-463
67770T. Itoh I-463.
120953CIP <- 1998, JCM <- T. Itoh: strain I-463

doi: 10.13145/bacdive6325.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Kineosporiales
  • family: Kineosporiaceae
  • genus: Kineosporia
  • species: Kineosporia mikuniensis
  • full scientific name: Kineosporia mikuniensis Kudo et al. 1998

@ref: 11511

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Kineosporiaceae

genus: Kineosporia

species: Kineosporia mikuniensis

full scientific name: Kineosporia mikuniensis Kudo et al. 1998

strain designation: I-463

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative94.13
120953positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
20055Pastel orange (2003)10-14 daysISP 2
20055Pastel orange (2003)10-14 daysISP 3
20055Pastel orange (2003)10-14 daysISP 4
20055Pastel orange (2003)10-14 daysISP 5
20055Pastel orange (2003)10-14 daysISP 6
20055Pastel orange (2003)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20055noISP 2
20055noISP 3
20055noISP 4
20055noISP 5
20055noISP 6
20055noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11511GYM 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
20055ISP 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
20055ISP 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:
20055ISP 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
20055ISP 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
20055ISP 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
20055ISP 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
41415MEDIUM 122 - for StreptomycesyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Yeast extract (2.000 g);Starch maize (10.000 g)
120953CIP Medium 122yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=122

culture temp

@refgrowthtypetemperaturerange
20055positiveoptimum28mesophilic
11511positivegrowth28mesophilic
41415positivegrowth30mesophilic
67770positivegrowth28mesophilic
120953positivegrowth15-37
120953nogrowth5psychrophilic
120953nogrowth41thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480no99.979

halophily

@refsaltgrowthtested relationconcentration
120953NaClpositivegrowth0 %
120953NaClnogrowth2 %
120953NaClnogrowth4 %
120953NaClnogrowth6 %
120953NaClnogrowth8 %
120953NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2005517234glucose+
2005522599arabinose+
2005517992sucrose+
2005518222xylose-
2005517268myo-inositol+
2005529864mannitol+
2005528757fructose+
2005526546rhamnose-
2005516634raffinose-
2005562968cellulose+
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol+builds acid from
6837118287L-fucose+builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose+builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
6837115443inulin-builds acid from
6837128053melibiose+builds acid from
6837117057cellobiose+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837130849L-arabinose+builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
1209534853esculin+hydrolysis
120953606565hippurate-hydrolysis
12095317632nitrate-reduction
12095316301nitrite-reduction
12095317632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12095335581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12095315688acetoin-
12095317234glucose+

enzymes

@refvalueactivityec
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
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
120953oxidase-
120953beta-galactosidase+3.2.1.23
120953alcohol dehydrogenase-1.1.1.1
120953catalase+1.11.1.6
120953gamma-glutamyltransferase+2.3.2.2
120953lysine decarboxylase-4.1.1.18
120953ornithine decarboxylase-4.1.1.17
120953phenylalanine ammonia-lyase-4.3.1.24
120953tryptophan deaminase-
120953urease+3.5.1.5

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20055+-+-++++-++++++++++
120953+++-+----++++-++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20055+++++-+--++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120953+-+/-++/-+/---+/-++++---+/-+/-----++++/-++/-+/-++/-+/--+/------++--++----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11511sphagnumMt. Mikuni in GummaJapanJPNAsia
67770SphagnumMt. Mikuni, Gunma Pref.JapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Moss
#Host#Plants#Peat moss

taxonmaps

  • @ref: 69479
  • File name: preview.99_63916.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_10254;97_12376;98_15213;99_63916&stattab=map
  • Last taxonomy: Kineosporia mikuniensis
  • 16S sequence: AB377117
  • Sequence Identity:
  • Total samples: 73
  • soil counts: 58
  • aquatic counts: 2
  • animal counts: 8
  • plant counts: 5

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
115111Risk group (German classification)
200551
1209531Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Kineosporia mikuniensis gene for 16S rRNA, partial sequence, strain: NBRC 16234
  • accession: AB377117
  • length: 1505
  • database: ena
  • NCBI tax ID: 499547

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kineosporia mikuniensis JCM 9961GCA_001315725contigncbi1307457
66792Kineosporia mikuniensis JCM 99611307457.3wgspatric1307457
66792Kineosporia mikuniensis JCM 99612734482001draftimg1307457

GC content

  • @ref: 11511
  • GC-content: 69.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno72.417no
gram-positiveno54.812no
anaerobicno94.339no
halophileno81.143no
spore-formingno95.537no
thermophileno99.025yes
glucose-utilyes86.642no
aerobicyes76.554no
flagellatedno90.334no
glucose-fermentyes51.12no

External links

@ref: 11511

culture collection no.: DSM 44390, JCM 9961, CIP 105755, IFO 16234, NBRC 16234

straininfo link

  • @ref: 75799
  • straininfo: 50608

literature

  • topic: Phylogeny
  • Pubmed-ID: 9828426
  • title: Description of four new species of the genus Kineosporia: Kineosporia succinea sp. nov., Kineosporia rhizophila sp. nov., Kineosporia mikuniensis sp. nov. and Kineosporia rhamnosa sp. nov., isolated from plant samples, and amended description of the genus Kineosporia.
  • authors: Kudo T, Matsushima K, Itoh T, Sasaki J, Suzuki K
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-48-4-1245
  • year: 1998
  • mesh: Actinomycetales/*classification/cytology/isolation & purification/physiology, Base Composition, DNA, Bacterial/chemistry, DNA, Ribosomal/chemistry, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plants/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Terminology as Topic, Vitamin K/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11511Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44390)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44390
20055Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44390.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
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
41415Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17809
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
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
75799Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50608.1StrainInfo: A central database for resolving microbial strain identifiers
120953Curators of the CIPCollection of Institut Pasteur (CIP 105755)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105755