Strain identifier
BacDive ID: 16098
Type strain: 
Species: Streptomyces violaceusniger
Strain history: KCC S-0850 <-- IFO 13459 <-- SAJ <-- ISP 5563 <-- NRRL B-1476.
NCBI tax ID(s): 68280 (species)
version 8.1 (current version)
General
@ref: 9645
BacDive-ID: 16098
DSM-Number: 40563
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic
description: Streptomyces violaceusniger DSM 40563 is a spore-forming, mesophilic bacterium that builds an aerial mycelium.
NCBI tax id
- NCBI tax id: 68280
- Matching level: species
strain history
| @ref | history |
|---|---|
| 9645 | <- E.B. Shirling, ISP <- NRRL |
| 67770 | KCC S-0850 <-- IFO 13459 <-- SAJ <-- ISP 5563 <-- NRRL B-1476. |
doi: 10.13145/bacdive16098.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Kitasatosporales
- family: Streptomycetaceae
- genus: Streptomyces
- species: Streptomyces violaceusniger
- full scientific name: Streptomyces violaceusniger corrig. (Waksman and Curtis 1916) Pridham et al. 1958 (Approved Lists 1980)
synonyms
@ref synonym 20215 Actinomyces violaceusniger 20215 Streptomyces violaceoniger
@ref: 9645
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces violaceusniger
full scientific name: Streptomyces violaceusniger (Waksman and Curtis 1916) Pridham et al. 1958 emend. Labeda and Lyons 1991
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 94.044 | |
| 69480 | 100 | positive |
colony morphology
| @ref | colony color | incubation period | medium used |
|---|---|---|---|
| 18658 | Yellow | 10-14 days | ISP 2 |
| 18658 | 10-14 days | ISP 3 | |
| 18658 | Yellow | 10-14 days | ISP 4 |
| 18658 | Yellow | 10-14 days | ISP 5 |
| 18658 | 10-14 days | ISP 6 | |
| 18658 | 10-14 days | ISP 7 |
multicellular morphology
| @ref | forms multicellular complex | complex name | complex color | medium name |
|---|---|---|---|---|
| 18658 | yes | Aerial Mycelium | Grey | ISP 2 |
| 18658 | yes | Aerial Mycelium | Grey | ISP 3 |
| 18658 | yes | Aerial Mycelium | Grey | ISP 4 |
| 18658 | yes | Aerial Mycelium | Grey | ISP 5 |
| 18658 | yes | Aerial Mycelium | White | ISP 6 |
| 18658 | yes | Aerial Mycelium | Grey | ISP 7 |
multimedia
- @ref: 9645
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40563.jpg
- caption: Medium 65 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 9645 | 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 |
| 18658 | ISP 2 | yes | Name: 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 | |
| 18658 | ISP 3 | yes | Name: 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: | |
| 18658 | ISP 4 | yes | Name: 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 | |
| 18658 | ISP 5 | yes | Name: 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 | |
| 18658 | ISP 6 | yes | Name: 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 | |
| 18658 | ISP 7 | yes | Name: 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 | |
| 9645 | ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 9645 | positive | growth | 28 | mesophilic |
| 18658 | positive | optimum | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore description | spore formation | confidence |
|---|---|---|---|
| 18658 | Formation of spore chains (spirales)(Sp), spore surface rugose | yes | |
| 69481 | yes | 100 | |
| 69480 | yes | 100 |
compound production
- @ref: 18658
- compound: Azalomycin F
halophily
- @ref: 18658
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity |
|---|---|---|---|
| 18658 | 17234 | glucose | + |
| 18658 | 22599 | arabinose | + |
| 18658 | 17992 | sucrose | - |
| 18658 | 18222 | xylose | - |
| 18658 | 17268 | myo-inositol | - |
| 18658 | 29864 | mannitol | + |
| 18658 | 28757 | fructose | + |
| 18658 | 26546 | rhamnose | + |
| 18658 | 16634 | raffinose | - |
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 9645 | 1 | Risk group (German classification) |
| 18658 | 1 | German classification |
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 67770 | Streptomyces violaceusniger gene for 16S rRNA, partial sequence, strain: NBRC 13459 | AB184420 | 1477 | ena | 68280 |
| 67770 | Streptomyces violaceusniger partial 16S rRNA gene, type strain NRRL B-1476T | AJ391822 | 1480 | ena | 68280 |
| 67770 | Streptomyces violaceusniger partial 16S rRNA gene, type strain ISP 5563T | AJ391823 | 1480 | ena | 68280 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Streptomyces violaceusniger strain NBRC 13459 | 68280.6 | wgs | patric | 68280 |
| 67770 | Streptomyces violaceusniger NBRC 13459 | GCA_005405945 | contig | ncbi | 68280 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 67770 | 70.7 | thermal denaturation, midpoint method (Tm) |
| 67770 | 71.2 | genome sequence analysis |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| gram-positive | yes | 86.517 | no |
| anaerobic | no | 99.1 | no |
| halophile | no | 91.286 | yes |
| spore-forming | yes | 94.761 | yes |
| glucose-util | yes | 90.85 | yes |
| flagellated | no | 98.287 | no |
| thermophile | no | 97.488 | no |
| aerobic | yes | 93.713 | no |
| glucose-ferment | no | 89.576 | no |
| motile | no | 93.498 | no |
External links
@ref: 9645
culture collection no.: DSM 40563, ATCC 27477, CBS 760.72, IFO 13459, ISP 5563, NBRC 13459, NRRL B-1476, RIA 1420, JCM 4850, BCRC 15178, CGMCC 4.1423, ICMP 734, LMG 19336, VKM Ac-583
straininfo link
- @ref: 85164
- straininfo: 92646
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19684315 | Streptomyces iranensis sp. nov., isolated from soil. | Hamedi J, Mohammadipanah F, Klenk HP, Potter G, Schumann P, Sproer C, von Jan M, Kroppenstedt RM | Int J Syst Evol Microbiol | 10.1099/ijs.0.015339-0 | 2009 | Base Sequence, Molecular Sequence Data, Phenotype, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification/physiology | Genetics |
| Phylogeny | 27379040 | Streptomyces antioxidans sp. nov., a Novel Mangrove Soil Actinobacterium with Antioxidative and Neuroprotective Potentials. | Ser HL, Tan LT, Palanisamy UD, Abd Malek SN, Yin WF, Chan KG, Goh BH, Lee LH | Front Microbiol | 10.3389/fmicb.2016.00899 | 2016 |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 9645 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40563) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-40563 | |
| 18658 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM40563.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |
| 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 | |
| 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) | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 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 | |
| 85164 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID92646.1 | StrainInfo: A central database for resolving microbial strain identifiers |