Strain identifier

BacDive ID: 6322

Type strain: Yes

Species: Kineosporia rhamnosa

Strain Designation: I-132

Strain history: CIP <- 1998, JCM <- T. Itoh: strain I-132

NCBI tax ID(s): 1307454 (strain), 84634 (species)

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General

@ref: 11508

BacDive-ID: 6322

DSM-Number: 44387

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

description: Kineosporia rhamnosa I-132 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from leaves of cat-taie .

NCBI tax id

NCBI tax idMatching level
1307454strain
84634species

strain history

@refhistory
11508<- JCM <- T. Itoh; I-132
67770T. Itoh I-132.
122181CIP <- 1998, JCM <- T. Itoh: strain I-132

doi: 10.13145/bacdive6322.20230509.8.1

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

@ref: 11508

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Kineosporiaceae

genus: Kineosporia

species: Kineosporia rhamnosa

full scientific name: Kineosporia rhamnosa Kudo et al. 1998

strain designation: I-132

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive99.999
122181positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19659Pastel orange10-14 daysISP 2
19659Pastel orange10-14 daysISP 3
19659yellow orange10-14 daysISP 4
19659Yellow orange10-14 daysISP 5
19659Yellow orange10-14 daysISP 6
19659Yellow orange10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19659noISP 2
19659noISP 3
19659noISP 4
19659noISP 5
19659noISP 6
19659noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11508GYM 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
19659ISP 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
19659ISP 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:
19659ISP 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
19659ISP 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
19659ISP 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
19659ISP 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
39351MEDIUM 122 - for StreptomycesyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Yeast extract (2.000 g);Starch maize (10.000 g)
122181CIP Medium 122yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=122

culture temp

@refgrowthtypetemperaturerange
19659positiveoptimum28mesophilic
11508positivegrowth28mesophilic
39351positivegrowth30mesophilic
67770positivegrowth28mesophilic
122181positivegrowth25-37mesophilic
122181nogrowth10psychrophilic
122181nogrowth41thermophilic
122181nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480no98.807

halophily

@refsaltgrowthtested relationconcentration
122181NaClpositivegrowth0 %
122181NaClnogrowth2 %
122181NaClnogrowth4 %
122181NaClnogrowth6 %
122181NaClnogrowth8 %
122181NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1965917234glucose+
1965922599arabinose+
1965917992sucrose+
1965918222xylose-
1965917268myo-inositol+
1965929864mannitol+
1965928757fructose+
1965926546rhamnose+
1965916634raffinose+
1965962968cellulose-
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
6837132528turanose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
683714853esculin+builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837116899D-mannitol-builds acid from
6837117266L-sorbose-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
6837117113erythritol-builds acid from
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
1221814853esculin-hydrolysis
122181606565hippurate-hydrolysis
12218117632nitrate-reduction
12218116301nitrite-reduction
12218117632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12218135581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
12218115688acetoin-
12218117234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
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
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
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
122181oxidase-
122181beta-galactosidase+3.2.1.23
122181alcohol dehydrogenase-1.1.1.1
122181gelatinase+/-
122181amylase-
122181DNase-
122181caseinase+3.4.21.50
122181catalase+1.11.1.6
122181tween esterase+
122181gamma-glutamyltransferase+2.3.2.2
122181lecithinase-
122181lipase-
122181lysine decarboxylase-4.1.1.18
122181ornithine decarboxylase-4.1.1.17
122181phenylalanine ammonia-lyase-4.3.1.24
122181protease-
122181tryptophan deaminase-
122181urease+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
19659+-+-++++++++++++---
122181+++++++-+++++-++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19659+++++-----+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122181+/--+/-+-+---+++/-+/--+/-+/-+/--+/----+/-+/-++/-+/------------+/-++/--+------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
11508leaves of cat-taie (Typha latifolia)Typha latifoliapond in SaitamaJapanJPNAsia
67770Leaves of cat-tail (Typha latifolia), pondTypha latifoliaSaitama Pref.JapanJPNAsia
122181Plant, Leaves of cat-tail, Typha latifoliaJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Leaf (Phyllosphere)

taxonmaps

  • @ref: 69479
  • File name: preview.99_90559.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_14411;97_17579;98_21847;99_90559&stattab=map
  • Last taxonomy: Kineosporia rhamnosa
  • 16S sequence: AB003935
  • Sequence Identity:
  • Total samples: 3443
  • soil counts: 2128
  • aquatic counts: 372
  • animal counts: 372
  • plant counts: 571

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
115081Risk group (German classification)
196591Hazard group
1221811Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Kineosporia rhamnosa gene for 16S rRNA, partial sequence, strain: I-132(=JCM9954)
  • accession: AB003935
  • length: 1474
  • database: ena
  • NCBI tax ID: 1307454

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kineosporia rhamnosa JCM 9954GCA_001315665contigncbi1307454
66792Kineosporia rhamnosa JCM 99541307454.6wgspatric1307454
66792Kineosporia rhamnosa JCM 99542734481998draftimg1307454

GC content

  • @ref: 11508
  • GC-content: 68.3
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes64.457no
gram-positiveyes84.974no
anaerobicno98.407no
halophileno96.864no
spore-formingyes61.141no
thermophileno99.739yes
glucose-utilyes88.036yes
aerobicyes94.526no
flagellatedno90.97no
glucose-fermentno90.43no

External links

@ref: 11508

culture collection no.: DSM 44387, JCM 9954, CIP 105752, IFO 16231, NBRC 16231

straininfo link

  • @ref: 75796
  • straininfo: 93051

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
11508Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44387)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44387
19659Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44387.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
39351Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17806
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
75796Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID93051.1StrainInfo: A central database for resolving microbial strain identifiers
122181Curators of the CIPCollection of Institut Pasteur (CIP 105752)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105752