Strain identifier

BacDive ID: 13208

Type strain: Yes

Species: Actinokineospora cibodasensis

Strain Designation: ID 03-0784

Strain history: <- NBRC; NBRC 104212 <- P. Lisdiyanti (LIPI)and K. Ando(NITE); ID 03-0784

NCBI tax ID(s): 547057 (species)

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General

@ref: 18015

BacDive-ID: 13208

DSM-Number: 45658

keywords: 16S sequence, Bacteria, spore-forming, mesophilic, Gram-positive, motile, rod-shaped

description: Actinokineospora cibodasensis ID 03-0784 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from litter.

NCBI tax id

  • NCBI tax id: 547057
  • Matching level: species

strain history

  • @ref: 18015
  • history: <- NBRC; NBRC 104212 <- P. Lisdiyanti (LIPI)and K. Ando(NITE); ID 03-0784

doi: 10.13145/bacdive13208.20230509.8.1

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 cibodasensis
  • full scientific name: Actinokineospora cibodasensis Lisdiyanti et al. 2010

@ref: 18015

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Actinokineospora

species: Actinokineospora cibodasensis

full scientific name: Actinokineospora cibodasensis Lisdiyanti et al. 2010

strain designation: ID 03-0784

type strain: yes

Morphology

cell morphology

  • @ref: 29447
  • gram stain: positive
  • cell width: 1.5-1.8 µm
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 29447
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
18015BENNETT'S AGAR (DSMZ Medium 548)yeshttps://mediadive.dsmz.de/medium/548Name: BENNETT'S AGAR (DSMZ Medium 548) Composition: Agar 15.0 g/l Glucose 10.0 g/l N-Z amine 2.0 g/l Yeast extract 1.0 g/l Beef extract 1.0 g/l Distilled water
18015GYM 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

culture temp

@refgrowthtypetemperaturerange
18015positivegrowth28mesophilic
29447positivegrowth25-28mesophilic
29447positiveoptimum25-28mesophilic

culture pH

@refabilitytypepH
29447positivegrowth7
29447positiveoptimum7

Physiology and metabolism

spore formation

  • @ref: 29447
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
29447NaClpositivegrowth1 %
29447NaClpositiveoptimum1 %

observation

  • @ref: 29447
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2944728757fructose+carbon source
2944728260galactose+carbon source
2944717234glucose+carbon source
2944717306maltose+carbon source
2944737684mannose+carbon source
2944717992sucrose+carbon source
2944727082trehalose+carbon source
294474853esculin+hydrolysis
2944717632nitrate+reduction
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369gelatinase+
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
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

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18015-----+--------------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
18015+----+/-++------------

Isolation, sampling and environmental information

isolation

  • @ref: 18015
  • sample type: litter
  • geographic location: West Java, Cibodas Botanical Garden
  • country: Indonesia
  • origin.country: IDN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Host#Plants
#Host Body Product#Plant#Plant litter (Forest)

Safety information

risk assessment

  • @ref: 18015
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 18015
  • description: Actinokineospora cibodasensis gene for 16S rRNA, partial sequence, strain: NBRC 104212
  • accession: AB447489
  • length: 1472
  • database: ena
  • NCBI tax ID: 547057

GC content

  • @ref: 18015
  • GC-content: 71.3

External links

@ref: 18015

culture collection no.: DSM 45658, BTCC B555, NBRC 104212

straininfo link

  • @ref: 82416
  • straininfo: 400394

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19933586Actinokineospora baliensis sp. nov., Actinokineospora cibodasensis sp. nov. and Actinokineospora cianjurensis sp. nov., isolated from soil and plant litter.Lisdiyanti P, Otoguro M, Ratnakomala S, Lestari Y, Hastuti RD, Triana E, Katsuhiko A, Widyastuti YInt J Syst Evol Microbiol10.1099/ijs.0.013276-02009Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Indonesia, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, Plants/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny24408526Alloactinosynnema iranicum sp. nov., a rare actinomycete isolated from a hypersaline wetland, and emended description of the genus Alloactinosynnema.Nikou MM, Ramezani M, Amoozegar MA, Fazeli SAS, Schumann P, Sproer C, Sanchez-Porro C, Ventosa AInt J Syst Evol Microbiol10.1099/ijs.0.049189-02014Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Iran, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry, *WetlandsGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
18015Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45658)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45658
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
29447Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2585328776041
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
82416Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400394.1StrainInfo: A central database for resolving microbial strain identifiers