Strain identifier

BacDive ID: 6323

Type strain: Yes

Species: Kineosporia succinea

Strain Designation: I-273

Strain history: CIP <- 1998, JCM <- T. Itoh: strain I-273

NCBI tax ID(s): 1307455 (strain), 84632 (species)

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General

@ref: 11509

BacDive-ID: 6323

DSM-Number: 44388

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

description: Kineosporia succinea I-273 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from fallen leaves.

NCBI tax id

NCBI tax idMatching level
84632species
1307455strain

strain history

@refhistory
11509<- JCM <- T. Itoh; I-273
67770T. Itoh I-273.
123364CIP <- 1998, JCM <- T. Itoh: strain I-273

doi: 10.13145/bacdive6323.20250331.9.3

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

@ref: 11509

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Kineosporiaceae

genus: Kineosporia

species: Kineosporia succinea

full scientific name: Kineosporia succinea Kudo et al. 1998

strain designation: I-273

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
123364positiveoval-shapedno
125439positive99.3

colony morphology

@refcolony colorincubation periodmedium used
20054Pastel orange (2003)10-14 daysISP 2
20054Pastel orange (2003)10-14 daysISP 3
20054Saffron yellow (1017)10-14 daysISP 4
20054Beige (1001)10-14 daysISP 5
20054Beige (1001)10-14 daysISP 6
20054Beige (1001)10-14 daysISP 7
123364

multicellular morphology

@refforms multicellular complexmedium name
20054noISP 2
20054noISP 3
20054noISP 4
20054noISP 5
20054noISP 6
20054noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11509GYM 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
20054ISP 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
20054ISP 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:
20054ISP 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
20054ISP 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
20054ISP 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
20054ISP 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
41414MEDIUM 122 - for StreptomycesyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Yeast extract (2.000 g);Starch maize (10.000 g)
123364CIP Medium 122yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=122

culture temp

@refgrowthtypetemperature
20054positiveoptimum28
11509positivegrowth28
41414positivegrowth30
67770positivegrowth28
123364positivegrowth15-30
123364nogrowth5
123364nogrowth37
123364nogrowth41

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
123364obligate aerobe
125439obligate aerobe98.9

halophily

@refsaltgrowthtested relationconcentration
123364NaClpositivegrowth0-4 %
123364NaClnogrowth6 %
123364NaClnogrowth8 %
123364NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2005417234glucose+
2005422599arabinose+
2005417992sucrose+
2005418222xylose-
2005417268myo-inositol-
2005429864mannitol+
2005428757fructose+
2005426546rhamnose+
2005416634raffinose-
2005462968cellulose+
12336416947citrate-carbon source
1233644853esculin-hydrolysis
123364606565hippurate-hydrolysis
12336417632nitrate-reduction
12336416301nitrite-reduction
12336417632nitrate-respiration
68371Potassium 5-ketogluconate-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837112936D-galactose+builds acid from
6837117754glycerol+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
6837116634raffinose-builds acid from
6837115443inulin-builds acid from
6837117992sucrose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine-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
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
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
12336435581indoleno
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-testindole test
12336415688acetoin-
12336417234glucose-
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382beta-glucuronidase-3.2.1.31
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+
68382cystine arylamidase+3.4.11.3
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
123364oxidase-
123364beta-galactosidase+3.2.1.23
123364alcohol dehydrogenase-1.1.1.1
123364gelatinase+/-
123364amylase+
123364DNase-
123364caseinase+3.4.21.50
123364catalase+1.11.1.6
123364tween esterase+
123364gamma-glutamyltransferase+2.3.2.2
123364lysine decarboxylase-4.1.1.18
123364ornithine decarboxylase-4.1.1.17
123364phenylalanine ammonia-lyase-4.3.1.24
123364tryptophan deaminase-
123364urease+3.5.1.5
68368urease+3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68382alpha-fucosidase+3.2.1.51
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20054+-++++++-++++-++-++
123364+++-+++--++++-++--+-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20054+++++-+--++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123364+-++-+---++++-+/--------+++++/-+/-+/-+/-++/--+/--+/-+/--+/-++/---++----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11509fallen leavesSaitamaJapanJPNAsia
67770Fallen leavesSaitama Pref.JapanJPNAsia

isolation source categories

  • Cat1: #Host Body-Site
  • Cat2: #Plant
  • Cat3: #Leaf (Phyllosphere)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
115091Risk group (German classification)
200541
1233641Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
11509Kineosporia succinea gene for 16S rRNA, partial sequence, strain: I-273(=JCM9957)AB0039321476nuccore1307455
67770Kineosporia succinea gene for 16S ribosomal RNA, partial sequence, strain: JCM 9957LC1139041459nuccore84632

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kineosporia succinea JCM 9957GCA_001315685contigncbi1307455
66792Kineosporia succinea JCM 99571307455.5wgspatric1307455
66792Kineosporia succinea JCM 99572734481999draftimg1307455
66792Kineosporia succinea DSM 443882923649072draftimg84632

GC content

  • @ref: 11509
  • GC-content: 70.7
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes80.414no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no85.374yes
125438spore-formingspore-formingAbility to form endo- or exosporesno50.764no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes76.116yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno89.335yes
125438motile2+flagellatedAbility to perform flagellated movementno70.227no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes56.8
125439BacteriaNetmotilityAbility to perform movementno83.2
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.3
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98.9

External links

@ref: 11509

culture collection no.: DSM 44388, JCM 9957, CIP 105753, IFO 16232, NBRC 16232

straininfo link

  • @ref: 75797
  • straininfo: 50606

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/urltitle
11509Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44388)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44388
20054Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44388.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
41414Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17807
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
75797Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50606.1StrainInfo: A central database for resolving microbial strain identifiers
123364Curators of the CIPCollection of Institut Pasteur (CIP 105753)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105753
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1