Strain identifier

BacDive ID: 13199

Type strain: Yes

Species: Actinokineospora diospyrosa

Strain history: IFO 15665 <-- T. Tamura YU8-1 <-- M. Hayakawa.

NCBI tax ID(s): 103728 (species)

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General

@ref: 11627

BacDive-ID: 13199

DSM-Number: 44255

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

description: Actinokineospora diospyrosa DSM 44255 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from fallen persimmon leaves.

NCBI tax id

  • NCBI tax id: 103728
  • Matching level: species

strain history

@refhistory
11627<- IFO <- T. Tamura, YU8-1
67771<- IFO <- T. Tamura YU8-1 <- M. Hayakawa
67770IFO 15665 <-- T. Tamura YU8-1 <-- M. Hayakawa.

doi: 10.13145/bacdive13199.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Actinokineospora
  • species: Actinokineospora diospyrosa
  • full scientific name: Actinokineospora diospyrosa Tamura et al. 1995

@ref: 11627

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Actinokineospora

species: Actinokineospora diospyrosa

full scientific name: Actinokineospora diospyrosa Tamura et al. 1995 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

  • @ref: 67771
  • gram stain: positive

colony morphology

@refcolony colorincubation periodmedium used
19639Red brown10-14 daysISP 2
19639Ivory10-14 daysISP 3
19639Sand yellow10-14 daysISP 4
19639Sand yellow10-14 daysISP 5
19639Light ivory10-14 daysISP 6
19639Ivory10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19639noISP 2
19639noISP 3
19639noISP 4
19639noISP 5
19639noISP 6
19639noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11627GYM 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
19639ISP 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
19639ISP 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:
19639ISP 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
19639ISP 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
19639ISP 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
19639ISP 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

culture temp

@refgrowthtypetemperaturerange
11627positivegrowth28mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

halophily

  • @ref: 19639
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

observation

@refobservation
67770quinones: MK-9(H4)
67771quinones: MK-9(H_4_)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1963917234glucose+
1963922599arabinose-
1963917992sucrose+
1963918222xylose-
1963917268myo-inositol-
1963929864mannitol-
1963928757fructose-
1963926546rhamnose-
1963916634raffinose-
1963962968cellulose-
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
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
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19639++++++-+-+----+-+--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19639-++++-+--++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11627fallen persimmon leavesYamanashi prefectureJapanJPNAsia
67770Fallen persimmon leavesYamanashi Pref.JapanJPNAsia
67771From fallen persimmon leavesYamanashi Pref.JapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body-Site#Plant#Leaf (Phyllosphere)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
116271Risk group (German classification)
196391Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Actinokineospora diospyrosa strain NRRL B-24047T 16S ribosomal RNA gene, partial sequence
  • accession: AF114797
  • length: 1512
  • database: ena
  • NCBI tax ID: 103728

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinokineospora diospyrosa DSM 442552596583538draftimg103728
66792Actinokineospora diospyrosa DSM 44255GCA_024171925scaffoldncbi103728

GC content

@refGC-contentmethod
1162769.3
6777069.3high performance liquid chromatography (HPLC)
6777070.3genome sequence analysis

External links

@ref: 11627

culture collection no.: DSM 44255, IFO 15665, JCM 9921, KCTC 9569, MTCC 2687, NBRC 15665, IMSNU 22098, NCIMB 13657, NRRL B-24047, VKM Ac-1984

straininfo link

  • @ref: 82407
  • straininfo: 50537

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11627Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44255)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44255
19639Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44255.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
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68368Automatically annotated from API 20E
68382Automatically annotated from API zym
82407Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50537.1StrainInfo: A central database for resolving microbial strain identifiers