Strain identifier
BacDive ID: 16997
Type strain: 
Species: Actinomadura chokoriensis
Strain Designation: 3-45-a(11)
Strain history: T. Kudo <-- I. Ara 3-45-a(11).
NCBI tax ID(s): 454156 (species)
version 8.1 (current version)
General
@ref: 16340
BacDive-ID: 16997
DSM-Number: 45346
keywords: 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive
description: Actinomadura chokoriensis 3-45-a is an aerobe, spore-forming, mesophilic bacterium that was isolated from sandy soil.
NCBI tax id
- NCBI tax id: 454156
- Matching level: species
strain history
| @ref | history |
|---|---|
| 16340 | <- JCM/RIKEN <- T. Kudo <- I. Ara; 3-45-a(11) |
| 67770 | T. Kudo <-- I. Ara 3-45-a(11). |
doi: 10.13145/bacdive16997.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Streptosporangiales
- family: Thermomonosporaceae
- genus: Actinomadura
- species: Actinomadura chokoriensis
- full scientific name: Actinomadura chokoriensis Ara et al. 2008
@ref: 16340
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Thermomonosporaceae
genus: Actinomadura
species: Actinomadura chokoriensis
full scientific name: Actinomadura chokoriensis Ara et al. 2008
strain designation: 3-45-a(11)
type strain: yes
Morphology
cell morphology
- @ref: 32467
- gram stain: positive
pigmentation
- @ref: 32467
- production: no
multimedia
- @ref: 16340
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45346.jpg
- caption: Medium 65 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 16340 | 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 |
| 16340 | N-Z-AMINE-MEDIUM (DSMZ Medium 554) | yes | https://mediadive.dsmz.de/medium/554 | Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water |
| 16340 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
| 16340 | BHI MEDIUM (DSMZ Medium 215) | yes | https://mediadive.dsmz.de/medium/215 | Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 16340 | positive | growth | 28 | mesophilic |
| 32467 | positive | growth | 20-45 | |
| 67770 | positive | growth | 28 | mesophilic |
culture pH
- @ref: 32467
- ability: positive
- type: growth
- pH: 05-09
- PH range: alkaliphile
Physiology and metabolism
oxygen tolerance
- @ref: 32467
- oxygen tolerance: aerobe
spore formation
- @ref: 32467
- spore formation: yes
halophily
- @ref: 32467
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 7 %
observation
- @ref: 67770
- observation: quinones: MK-9(H6), MK-9(H8), MK-9(H4)
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32467 | 22599 | arabinose | + | carbon source |
| 32467 | 17057 | cellobiose | + | carbon source |
| 32467 | 28757 | fructose | + | carbon source |
| 32467 | 17754 | glycerol | + | carbon source |
| 32467 | 29864 | mannitol | + | carbon source |
| 32467 | 17992 | sucrose | + | carbon source |
| 32467 | 18222 | xylose | + | carbon source |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 16340 | sandy soil | Chokoria, Cox's Bazar | Bangladesh | BGD | Asia |
| 67770 | Sandy soil | Chokoria, Cox's Bazar | Bangladesh | BGD | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Sandy |
| #Environmental | #Terrestrial | #Soil |
Safety information
risk assessment
- @ref: 16340
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16340
- description: Actinomadura chokoriensis gene for 16S rRNA, partial sequence
- accession: AB331730
- length: 1501
- database: ena
- NCBI tax ID: 454156
GC content
| @ref | GC-content | method |
|---|---|---|
| 16340 | 72.43 | |
| 67770 | 72.43 | high performance liquid chromatography (HPLC) |
External links
@ref: 16340
culture collection no.: DSM 45346, JCM 13932, MTCC 8056
straininfo link
- @ref: 85999
- straininfo: 403763
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 18599711 | Actinomadura bangladeshensis sp. nov. and Actinomadura chokoriensis sp. nov. | Ara I, Matsumoto A, Bakir MA, Kudo T, Omura S, Takahashi Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.65533-0 | 2008 | Actinomycetales/*classification/genetics/growth & development/ultrastructure, Bangladesh, Microscopy, Electron, Scanning, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species Specificity | Genetics |
| Phylogeny | 22021584 | Actinomadura geliboluensis sp. nov., isolated from soil. | Sazak A, Camas M, Sproer C, Klenk HP, Sahin N | Int J Syst Evol Microbiol | 10.1099/ijs.0.036145-0 | 2011 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Carbohydrates/analysis, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/analysis, *Soil Microbiology, Turkey | Genetics |
| Phylogeny | 25678680 | Actinomadura darangshiensis sp. nov., isolated from a volcanic cone. | Lee SD, Kim SB | Int J Syst Evol Microbiol | 10.1099/ijs.0.000099 | 2015 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry, Volcanic Eruptions | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 16340 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45346) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45346 | |||
| 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 | |||
| 32467 | 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 | 28688 | 28776041 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 85999 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID403763.1 | StrainInfo: A central database for resolving microbial strain identifiers |