Strain identifier

BacDive ID: 6324

Type strain: Yes

Species: Kineosporia rhizophila

Strain Designation: I-449

Strain history: CIP <- 1998, JCM <- T. Itoh: strain I-449

NCBI tax ID(s): 1307456 (strain), 84633 (species)

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General

@ref: 11510

BacDive-ID: 6324

DSM-Number: 44389

keywords: 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive, motile, oval-shaped

description: Kineosporia rhizophila I-449 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from root of galingale .

NCBI tax id

NCBI tax idMatching level
1307456strain
84633species

strain history

@refhistory
11510<- JCM <- T. Itoh; I-449
67770T. Itoh I-449.
122200CIP <- 1998, JCM <- T. Itoh: strain I-449

doi: 10.13145/bacdive6324.20230509.8.1

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 rhizophila
  • full scientific name: Kineosporia rhizophila Kudo et al. 1998

@ref: 11510

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Kineosporiaceae

genus: Kineosporia

species: Kineosporia rhizophila

full scientific name: Kineosporia rhizophila Kudo et al. 1998

strain designation: I-449

type strain: yes

Morphology

cell morphology

  • @ref: 122200
  • gram stain: positive
  • cell shape: oval-shaped
  • motility: yes

colony morphology

@refcolony colorincubation periodmedium used
19660Signal orange10-14 daysISP 2
19660Signal orange10-14 daysISP 3
19660Yellow orange10-14 daysISP 4
19660Yellow orange10-14 daysISP 5
19660Signal orange10-14 daysISP 6
19660Signal orange10-14 daysISP 7
122200

multicellular morphology

@refforms multicellular complexmedium name
19660noISP 2
19660noISP 3
19660noISP 4
19660noISP 5
19660noISP 6
19660noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11510GYM 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
19660ISP 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
19660ISP 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:
19660ISP 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
19660ISP 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
19660ISP 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
19660ISP 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
39353MEDIUM 122 - for StreptomycesyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Yeast extract (2.000 g);Starch maize (10.000 g)
122200CIP Medium 122yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=122

culture temp

@refgrowthtypetemperaturerange
19660positiveoptimum28mesophilic
11510positivegrowth28mesophilic
39353positivegrowth30mesophilic
67770positivegrowth28mesophilic
122200positivegrowth30-41
122200nogrowth10psychrophilic
122200nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122200
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
122200NaClpositivegrowth0-2 %
122200NaClnogrowth4 %
122200NaClnogrowth6 %
122200NaClnogrowth8 %
122200NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1966017234glucose+
1966022599arabinose+
1966017992sucrose+
1966018222xylose-
1966017268myo-inositol-
1966029864mannitol+
1966028757fructose+
1966026546rhamnose+
1966016634raffinose+
1966062968cellulose+
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
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117057cellobiose+builds acid from
683714853esculin+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
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-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
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose+builds acid from
6837117108D-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
12220016947citrate-carbon source
1222004853esculin+hydrolysis
122200606565hippurate-hydrolysis
12220017632nitrate+reduction
12220016301nitrite-reduction
12220017632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12220035581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12220015688acetoin-
12220017234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
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
68382valine arylamidase+
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
122200oxidase-
122200beta-galactosidase+3.2.1.23
122200alcohol dehydrogenase-1.1.1.1
122200gelatinase-
122200amylase-
122200caseinase-3.4.21.50
122200catalase+1.11.1.6
122200tween esterase+
122200gamma-glutamyltransferase+2.3.2.2
122200lecithinase-
122200lipase-
122200lysine decarboxylase-4.1.1.18
122200ornithine decarboxylase-4.1.1.17
122200phenylalanine ammonia-lyase-4.3.1.24
122200tryptophan deaminase-
122200urease+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
19660+-+-++++-++++++++--
122200+++-++---++++-++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19660+++++-+--++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122200+--+-+---++++-+/---------+/-++/-++/-+/-+/-+/---+/------+/-----+----

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
11510root of galingale (Cyperus microiria)Cyperus microiriaSaitamaJapanJPNAsia
67770Root of galingale (Cyperus microiria)Cyperus microiriaSaitama Pref.JapanJPNAsia
122200Plant, Root of galingale, Cyperus microiriaSaitamaJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
115101Risk group (German classification)
196601Hazard group
1222001Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Kineosporia rhizophila partial 16S rRNA gene, type strain DSM 44389T, clone 1FR7499861506ena1307456
20218Kineosporia rhizophila partial 16S rRNA gene, type strain DSM 44389T, clone 2FR7499871506ena1307456
20218Kineosporia rhizophila partial 16S rRNA gene, type strain DSM 44389T, clone 3FR7499881506ena1307456
11510Kineosporia rhizophila gene for 16S rRNA, partial sequence, strain: I-449(=JCM9960)AB0039331432ena1307456

GC content

  • @ref: 11510
  • GC-content: 70
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 11510

culture collection no.: DSM 44389, JCM 9960, CIP 105754, IFO 16233, NBRC 16233

straininfo link

  • @ref: 75798
  • straininfo: 264376

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
11510Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44389)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44389
19660Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44389.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
39353Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17808
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
75798Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID264376.1StrainInfo: A central database for resolving microbial strain identifiers
122200Curators of the CIPCollection of Institut Pasteur (CIP 105754)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105754