Strain identifier
BacDive ID: 13209
Type strain: 
Species: Actinokineospora cianjurensis
Strain Designation: ID 03-0810
Strain history: <- NBRC; NBRC 105526 <- P. Lisdiyanti (LIPI)and K. Ando(NITE); ID 03-0810
NCBI tax ID(s): 585224 (species)
version 8.1 (current version)
General
@ref: 18014
BacDive-ID: 13209
DSM-Number: 45657
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, Gram-positive, motile, rod-shaped
description: Actinokineospora cianjurensis ID 03-0810 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from leaf-litter.
NCBI tax id
- NCBI tax id: 585224
- Matching level: species
strain history
- @ref: 18014
- history: <- NBRC; NBRC 105526 <- P. Lisdiyanti (LIPI)and K. Ando(NITE); ID 03-0810
doi: 10.13145/bacdive13209.20230509.8.1
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 cianjurensis
- full scientific name: Actinokineospora cianjurensis Lisdiyanti et al. 2010
@ref: 18014
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Pseudonocardiaceae
genus: Actinokineospora
species: Actinokineospora cianjurensis
full scientific name: Actinokineospora cianjurensis Lisdiyanti et al. 2010
strain designation: ID 03-0810
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|
| 29447 | positive | 1.5-2 µm | rod-shaped | yes | |
| 69480 | positive | 100 |
pigmentation
- @ref: 29447
- production: yes
Culture and growth conditions
culture medium
- @ref: 18014
- name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
- growth: yes
- link: https://mediadive.dsmz.de/medium/65
- composition: Name: 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
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 29447 | positive | growth | 25-28 | mesophilic |
| 29447 | positive | optimum | 25-28 | mesophilic |
| 18014 | positive | growth | 28 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 29447 | positive | growth | 7 |
| 29447 | positive | optimum | 7 |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 29447 | yes | |
| 69481 | yes | 100 |
| 69480 | yes | 100 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 29447 | NaCl | positive | growth | 1 % |
| 29447 | NaCl | positive | optimum | 1 % |
observation
- @ref: 29447
- observation: aggregates in chains
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29447 | 28757 | fructose | + | carbon source |
| 29447 | 28260 | galactose | + | carbon source |
| 29447 | 17234 | glucose | + | carbon source |
| 29447 | 17306 | maltose | + | carbon source |
| 29447 | 37684 | mannose | + | carbon source |
| 29447 | 17992 | sucrose | + | carbon source |
| 29447 | 27082 | trehalose | + | carbon source |
| 29447 | 4853 | esculin | + | hydrolysis |
| 29447 | 17632 | nitrate | + | reduction |
Isolation, sampling and environmental information
isolation
- @ref: 18014
- sample type: leaf-litter
- geographic location: West Java, Cibodas Botanical Garden
- country: Indonesia
- origin.country: IDN
- continent: Asia
isolation source categories
- Cat1: #Host Body-Site
- Cat2: #Plant
- Cat3: #Leaf (Phyllosphere)
taxonmaps
- @ref: 69479
- File name: preview.99_119928.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_394;97_444;98_80846;99_119928&stattab=map
- Last taxonomy: Actinokineospora
- 16S sequence: AB473945
- Sequence Identity:
- Total samples: 113
- soil counts: 62
- aquatic counts: 7
- animal counts: 12
- plant counts: 32
Safety information
risk assessment
- @ref: 18014
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 18014
- description: Actinokineospora cianjurensis gene for 16S rRNA, partial sequence, strain: BTCC B-558
- accession: AB473945
- length: 1477
- database: ena
- NCBI tax ID: 585224
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Actinokineospora cianjurensis DSM 45657 | GCA_003663795 | scaffold | ncbi | 585224 |
| 66792 | Actinokineospora cianjurensis strain DSM 45657 | 585224.3 | wgs | patric | 585224 |
| 66792 | Actinokineospora cianjurensis DSM 45657 | 2734482175 | draft | img | 585224 |
GC content
- @ref: 18014
- GC-content: 70.2
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | yes | 52.574 | no |
| flagellated | no | 87.282 | no |
| gram-positive | yes | 86.016 | no |
| anaerobic | no | 99.078 | no |
| aerobic | yes | 90.781 | no |
| halophile | no | 93.999 | yes |
| spore-forming | yes | 92.185 | yes |
| glucose-util | yes | 87.688 | no |
| thermophile | no | 96.946 | yes |
| glucose-ferment | no | 92.003 | no |
External links
@ref: 18014
culture collection no.: DSM 45657, BTCC B-558, NBRC 105526
straininfo link
- @ref: 82417
- straininfo: 401597
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19933586 | Actinokineospora 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 Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.013276-0 | 2009 | Actinomycetales/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 Microbiology | Genetics |
| Phylogeny | 32618556 | Actinokineospora pegani sp. nov., an endophytic actinomycete isolated from the surface-sterilized root of Peganum harmala L. | Lei YJ, Xia ZF, Luo XX, Zhang LL | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004299 | 2020 | Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Peganum/*microbiology, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 18014 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45657) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45657 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 29447 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25853 | 28776041 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69479 | João 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 | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 82417 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID401597.1 | StrainInfo: A central database for resolving microbial strain identifiers |