Strain identifier
BacDive ID: 13208
Type strain:
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)
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
@ref | name | growth | link | composition |
---|---|---|---|---|
18015 | BENNETT'S AGAR (DSMZ Medium 548) | yes | https://mediadive.dsmz.de/medium/548 | Name: 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 |
18015 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://mediadive.dsmz.de/medium/65 | 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 |
---|---|---|---|---|
18015 | positive | growth | 28 | mesophilic |
29447 | positive | growth | 25-28 | mesophilic |
29447 | positive | optimum | 25-28 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
29447 | positive | growth | 7 |
29447 | positive | optimum | 7 |
Physiology and metabolism
spore formation
- @ref: 29447
- spore formation: yes
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 |
68369 | 25115 | malate | - | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | - | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | - | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | - | assimilation |
68369 | 5291 | gelatin | + | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | + | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68369 | gelatinase | + | |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68382 | esterase (C 4) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18015 | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
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 | 24408526 | Alloactinosynnema 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 A | Int J Syst Evol Microbiol | 10.1099/ijs.0.049189-0 | 2014 | Actinomycetales/*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, *Wetlands | Genetics |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
18015 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45658) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45658 | |||
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 | |
68369 | Automatically annotated from API 20NE | |||||
68382 | Automatically annotated from API zym | |||||
82416 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID400394.1 | StrainInfo: A central database for resolving microbial strain identifiers |