Strain identifier

BacDive ID: 6316

Type strain: Yes

Species: Kineococcus aurantiacus

Strain Designation: RA 333

Strain history: CIP <- 1998, Yokota, IFO, Osaka, Japan: strain RA 333

NCBI tax ID(s): 37633 (species)

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General

@ref: 3186

BacDive-ID: 6316

DSM-Number: 7487

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

description: Kineococcus aurantiacus RA 333 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 37633
  • Matching level: species

strain history

@refhistory
3186<- IFO
401411998, Yokota, IFO, Osaka, Japan: strain RA 333
67770IFO 15268 <-- T. Tamura RA 333.
116562CIP <- 1998, Yokota, IFO, Osaka, Japan: strain RA 333

doi: 10.13145/bacdive6316.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Kineosporiales
  • family: Kineosporiaceae
  • genus: Kineococcus
  • species: Kineococcus aurantiacus
  • full scientific name: Kineococcus aurantiacus Yokota et al. 1993

@ref: 3186

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Kineosporiaceae

genus: Kineococcus

species: Kineococcus aurantiacus

full scientific name: Kineococcus aurantiacus Yokota et al. 1993

strain designation: RA 333

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
116562positivecoccus-shapedyes

colony morphology

@refcolony colorincubation periodmedium used
19728Yellow orange10-14 days5006
1972810-14 days5425
19728Pale orange10-14 days5428
19728Pale orange10-14 days5530
19728Yellow orange10-14 daysISP 2
19728Pastel yellow10-14 daysISP 4
19728Yellow orange10-14 daysISP 6

multicellular morphology

@refforms multicellular complexmedium name
19728noISP 2
19728noISP 4
19728noISP 6
19728no5006
19728no5425
19728no5428
19728no5530

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3186GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65; with strain-specific modifications) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Distilled water
19728ISP 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
19728ISP 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
19728ISP 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
197285006yesMedium: 5006 Name: Composition (g/l) Sucrose 3,0 Dextrin 15,0 Meat extract 1,0 Yeast extract 2,0 Tryptone soy broth (Oxoid) 5,0 NaCl 0,5 K2HPO4 0,5 MgSO4 x 7 H2O 0,5 FeSO4 x 7 H2O 0,01 Agar 20,0 Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7,3 Usage: Maintenance Organisms: All Actinomycetes
197285425yesName: Brain Heart Infusion (BHI) Agar; 5425 Composition: Calf brain infusion 200.0 g/l Beef heart infusion 250.0 g/l Casein (meat) peptone 10.0 g/l Glucose 2.0 g/l NaCl 5.0 g/l Na2HPO4 2.5 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.4 Usage: Maintenance and revitalization Organisms: Dermatophilus congolensis, Nocardia brasieliensis, N. asteroides, Rhodococcus equi, R. fascians, R. rhodochrous, Streptomyces thermoviol aceus subsp. apingens, Coryneform species
197285428yes
197285530yes
40141MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicumyesDistilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)
116562CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116
116562CIP Medium 194yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=194

culture temp

@refgrowthtypetemperaturerange
3186positivegrowth30mesophilic
40141positivegrowth30mesophilic
56395positivegrowth30mesophilic
67770positivegrowth28mesophilic
116562positivegrowth22-37
116562nogrowth5psychrophilic
116562nogrowth15psychrophilic
116562nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
56395microaerophile
116562obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 98.875

halophily

@refsaltgrowthtested relationconcentration
19728NaClpositivemaximum2.5 %
116562NaClpositivegrowth0-4 %
116562NaClnogrowth6 %
116562NaClnogrowth8 %
116562NaClnogrowth10 %

murein

  • @ref: 3186
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

observation

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

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
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371salicin-builds acid from17814
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
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-ribose-builds acid from16988
68371D-arabinose-builds acid from17108
68371glycerol-builds acid from17754
68368gelatin-hydrolysis5291
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368citrate-assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
116562citrate-carbon source16947
116562esculin+hydrolysis4853
116562hippurate-hydrolysis606565
116562nitrate-reduction17632
116562nitrite-reduction16301
116562nitrate-respiration17632
68379nitrate+reduction17632
68379esculin+hydrolysis4853
68379urea-hydrolysis16199
68379gelatin-hydrolysis5291
68379D-glucose+fermentation17634
68379D-ribose+fermentation16988
68379D-xylose+fermentation65327
68379D-mannitol+fermentation16899
68379maltose+fermentation17306
68379lactose+fermentation17716
68379sucrose-fermentation17992
68379glycogen+fermentation28087

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
11656235581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
11656215688acetoin-
11656217234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382lipase (C 14)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
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
116562oxidase-
116562beta-galactosidase+3.2.1.23
116562alcohol dehydrogenase-1.1.1.1
116562gelatinase-
116562amylase-
116562DNase-
116562caseinase-3.4.21.50
116562catalase+1.11.1.6
116562tween esterase-
116562gamma-glutamyltransferase-2.3.2.2
116562lecithinase-
116562lipase-
116562lysine decarboxylase-4.1.1.18
116562ornithine decarboxylase-4.1.1.17
116562phenylalanine ammonia-lyase-4.3.1.24
116562tryptophan deaminase-
116562urease+3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19728+--+-+--+--++++++-+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19728+++------++--------
116562++--+----++-+--+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19728---------+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116562-+/--+/--+/---+/-+/-+/-+/-+/-----------+/-+/--+/----+/-------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116562---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
3186soilIndore regionIndiaINDAsia
56395SoilIndoreIndiaINDAsia1983
67770SoilIndiaINDAsia
116562Environment, SoilIndoreIndiaINDAsia1983

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_89202.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_36963;97_46976;98_61576;99_89202&stattab=map
  • Last taxonomy: Kineococcus
  • 16S sequence: D17527
  • Sequence Identity:
  • Total samples: 343
  • soil counts: 89
  • aquatic counts: 42
  • animal counts: 128
  • plant counts: 84

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
31861Risk group (German classification)
197281Risk group (German classification)
1165621Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Kineococcus aurantiacus gene for 16S rRNA, partial sequenceAB0074201409ena37633
20218Kineococcus aurantiacus gene for 16S ribosomal RNA, partial sequenceD175271394ena37633
20218K.aurantiacus (IFO 15268) 16S rRNA geneX779581417ena37633

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kineococcus aurantiacus strain DSM 748737633.4wgspatric37633
66792Kineococcus aurantiacus DSM 74872844801912draftimg37633
67770Kineococcus aurantiacus DSM 7487GCA_013409345contigncbi37633

GC content

@refGC-contentmethod
318674.0high performance liquid chromatography (HPLC)
6777073.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno54no
gram-positiveyes91.969no
anaerobicno99.173yes
halophileno91.284no
spore-formingno81.111no
glucose-utilyes86.991no
aerobicyes90.199yes
flagellatedno87.671no
thermophileno99.439no
motileyes71.42no
glucose-fermentno70.535yes

External links

@ref: 3186

culture collection no.: DSM 7487, ATCC 51238, IFO 15268, NBRC 15268, CCUG 44589, CIP 105426, JCM 10180, CCM 4366, NCFB 3013, NCIMB 13309, VKM Ac-1947

straininfo link

  • @ref: 75790
  • straininfo: 42870

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12054260Kineococcus radiotolerans sp. nov., a radiation-resistant, gram-positive bacterium.Phillips RW, Wiegel J, Berry CJ, Fliermans C, Peacock AD, White DC, Shimkets LJInt J Syst Evol Microbiol10.1099/00207713-52-3-9332002Actinomycetales/*classification/genetics/*physiology/radiation effects, Bacterial Typing Techniques, DNA, Ribosomal/analysis, Desiccation, Gamma Rays, Molecular Sequence Data, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, *Radiation Tolerance, Sequence Analysis, DNAGenetics
Phylogeny19605726Kineococcus rhizosphaerae sp. nov., isolated from rhizosphere soil.Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.008599-02009Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Aerobiosis, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/metabolism, Phospholipids/analysis, Phylogeny, Pigments, Biological/biosynthesis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisEnzymology
Phylogeny22669199Kineococcus endophytica sp. nov., a novel endophytic actinomycete isolated from a coastal halophyte in Jiangsu, China.Bian GK, Feng ZZ, Qin S, Xing K, Wang Z, Cao CL, Liu CH, Dai CC, Jiang JHAntonie Van Leeuwenhoek10.1007/s10482-012-9757-42012Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Salt-Tolerant Plants/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
Phylogeny26232950Kineococcus gypseus sp. nov., isolated from saline sediment.Li Q, Li G, Chen X, Xu F, Li Y, Xu L, Jiang Y, Jiang CInt J Syst Evol Microbiol10.1099/ijsem.0.0004782015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny26703438Kineococcus mangrovi sp. nov., isolated from mangrove sediment.Duangmal K, Muangham S, Mingma R, Yimyai T, Srisuk N, Kitpreechavanich V, Matsumoto A, Takahashi YInt J Syst Evol Microbiol10.1099/ijsem.0.0008602015
Phylogeny28984560Kineococcus terrestris sp. nov. and Kineococcus aureolus sp. nov., isolated from saline sediment.Xu FJ, Li QY, Li GD, Chen X, Jiang Y, Jiang CLInt J Syst Evol Microbiol10.1099/ijsem.0.0023802017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny33036385Kineococcus vitellinus sp. nov., Kineococcus indalonis sp. nov. and Kineococcus siccus sp. nov., Isolated Nearby the Tabernas Desert (Almeria, Spain).Molina-Menor E, Gimeno-Valero H, Pascual J, Pereto J, Porcar MMicroorganisms10.3390/microorganisms81015472020

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3186Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7487)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7487
19728Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM7487.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
40141Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17444
56395Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 44589)https://www.ccug.se/strain?id=44589
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
68379Automatically annotated from API Coryne
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)
75790Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42870.1StrainInfo: A central database for resolving microbial strain identifiers
116562Curators of the CIPCollection of Institut Pasteur (CIP 105426)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105426