Strain identifier
BacDive ID: 16077
Type strain:
Species: Streptomyces violaceochromogenes
Strain history: KCC S-0530 <-- IFO 13100 <-- SAJ <-- ISP 5181 <-- T. P. Preobrazhenskaya INA 425.
NCBI tax ID(s): 67377 (species)
General
@ref: 9245
BacDive-ID: 16077
DSM-Number: 40181
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic
description: Streptomyces violaceochromogenes DSM 40181 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.
NCBI tax id
- NCBI tax id: 67377
- Matching level: species
strain history
@ref | history |
---|---|
9245 | <- E.B. Shirling, ISP <- T.P. Preobrazhenskaya, INA |
67770 | KCC S-0530 <-- IFO 13100 <-- SAJ <-- ISP 5181 <-- T. P. Preobrazhenskaya INA 425. |
doi: 10.13145/bacdive16077.20230509.8.1
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 violaceochromogenes
- full scientific name: Streptomyces violaceochromogenes (Ryabova and Preobrazhenskaya 1957) Pridham 1970 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Actinomyces violaceochromogenes
@ref: 9245
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces violaceochromogenes
full scientific name: Streptomyces violaceochromogenes (Ryabova and Preobrazhenskaya 1957) Pridham 1970
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | no | 95.071 | |
69480 | 100 | positive |
colony morphology
@ref | colony color | incubation period | medium used |
---|---|---|---|
19419 | Brown | 10-14 days | ISP 2 |
19419 | Yellow | 10-14 days | ISP 3 |
19419 | Brown | 10-14 days | ISP 4 |
19419 | Yellow | 10-14 days | ISP 5 |
19419 | Yellow | 10-14 days | ISP 6 |
19419 | Brown | 10-14 days | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | complex name | complex color | medium name |
---|---|---|---|---|
19419 | yes | Aerial Mycelium | White | ISP 2 |
19419 | yes | Aerial Mycelium | Grey | ISP 3 |
19419 | yes | Aerial Mycelium | Grey | ISP 4 |
19419 | yes | Aerial Mycelium | Grey | ISP 5 |
19419 | no | ISP 6 | ||
19419 | yes | Aerial Mycelium | Grey | ISP 7 |
multimedia
- @ref: 9245
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40181.jpg
- caption: Medium 65 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
9245 | 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 |
19419 | 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 | |
19419 | 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: | |
19419 | 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 | |
19419 | 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 | |
19419 | 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 | |
19419 | 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 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
9245 | positive | growth | 28 | mesophilic |
19419 | positive | optimum | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore description | spore formation | confidence |
---|---|---|---|
19419 | Formation of spore chains: retinaculiapetri, spore surface: smooth | yes | |
69481 | yes | 100 | |
69480 | yes | 100 |
halophily
- @ref: 19419
- salt: NaCl
- growth: positive
- tested relation: maximum
- concentration: 7.5 %
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
19419 | 62968 | cellulose | - | |
19419 | 16634 | raffinose | - | |
19419 | 26546 | rhamnose | - | |
19419 | 28757 | fructose | - | |
19419 | 29864 | mannitol | - | |
19419 | 17268 | myo-inositol | - | |
19419 | 18222 | xylose | - | |
19419 | 17992 | sucrose | - | |
19419 | 22599 | arabinose | - | |
19419 | 17234 | glucose | + | |
68368 | 5291 | gelatin | - | hydrolysis |
68368 | 27897 | tryptophan | - | energy source |
68368 | 16199 | urea | - | hydrolysis |
68368 | 16947 | citrate | - | assimilation |
68368 | 18257 | ornithine | - | degradation |
68368 | 25094 | lysine | - | degradation |
68368 | 29016 | arginine | - | hydrolysis |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 15688 | acetoin | yes |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | yes |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68368 | 15688 | acetoin | + | |
68368 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68368 | gelatinase | - | |
68368 | tryptophan deaminase | + | 4.1.99.1 |
68368 | urease | - | 3.5.1.5 |
68368 | ornithine decarboxylase | - | 4.1.1.17 |
68368 | lysine decarboxylase | - | 4.1.1.18 |
68368 | arginine dihydrolase | - | 3.5.3.6 |
68368 | beta-galactosidase | + | 3.2.1.23 |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL |
---|---|---|---|---|---|---|---|---|---|---|---|
19419 | + | - | - | - | - | + | - | + | - | + | - |
Isolation, sampling and environmental information
isolation
- @ref: 9245
- sample type: soil
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
9245 | 1 | Risk group (German classification) |
19419 | 1 | Risk group (German classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Streptomyces sp. NTG2 gene for 16S ribosomal RNA, partial sequence | AB920573 | 1252 | ena | 1571709 |
20218 | Streptomyces sp. NTG5 gene for 16S ribosomal RNA, partial sequence | AB920576 | 1286 | ena | 1571712 |
20218 | Streptomyces sp. NTGn11 gene for 16S ribosomal RNA, partial sequence | AB920578 | 1303 | ena | 1571714 |
20218 | Streptomyces sp. NTHn1 gene for 16S ribosomal RNA, partial sequence | AB920579 | 1306 | ena | 1571715 |
20218 | Streptomyces sp. NTHn2 gene for 16S ribosomal RNA, partial sequence | AB920580 | 1312 | ena | 1571716 |
20218 | Streptomyces sp. NTM2 gene for 16S ribosomal RNA, partial sequence | AB920583 | 1297 | ena | 1571719 |
20218 | Streptomyces sp. MTMn4 gene for 16S ribosomal RNA, partial sequence | AB920585 | 1279 | ena | 1571721 |
20218 | Streptomyces sp. NTRH1 gene for 16S ribosomal RNA, partial sequence | AB920586 | 1287 | ena | 1571722 |
20218 | Streptomyces violaceochromogenes strain IFO 13100 16S ribosomal RNA gene, partial sequence | AY999867 | 1425 | ena | 67377 |
20218 | Streptomyces violaceochromogenes gene for 16S ribosomal RNA, partial sequence, strain: JCM 4530 | D44215 | 121 | ena | 67377 |
20218 | Streptomyces violaceochromogenes gene for 16S rRNA, partial sequence, strain: NBRC 13100 | AB184312 | 1477 | ena | 67377 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Streptomyces violaceochromogenes JCM 4530 | GCA_014650235 | scaffold | ncbi | 67377 |
66792 | Streptomyces violaceochromogenes strain JCM 4530 | 67377.3 | wgs | patric | 67377 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
flagellated | no | 98.081 | no |
gram-positive | yes | 89.643 | no |
anaerobic | no | 99.049 | no |
aerobic | yes | 92.163 | no |
halophile | no | 93.571 | no |
spore-forming | yes | 95.045 | yes |
glucose-util | yes | 90.208 | yes |
thermophile | no | 98.18 | yes |
motile | no | 93.741 | no |
glucose-ferment | no | 90.544 | no |
External links
@ref: 9245
culture collection no.: DSM 40181, ATCC 19932, ATCC 25512, CBS 654.69, IFO 13100, INA 425, ISP 5181, NBRC 13100, RIA 1292, JCM 4530, CGMCC 4.1753, KCTC 19974, NRRL B-5427, VKM Ac-581
straininfo link
- @ref: 85147
- straininfo: 45813
literature
- topic: Pathogenicity
- Pubmed-ID: 30797881
- title: Nybomycin-producing Streptomyces isolated from carpenter ant Camponotus vagus.
- authors: Zakalyukina YV, Birykov MV, Lukianov DA, Shiriaev DI, Komarova ES, Skvortsov DA, Kostyukevich Y, Tashlitsky VN, Polshakov VI, Nikolaev E, Sergiev PV, Osterman IA
- journal: Biochimie
- DOI: 10.1016/j.biochi.2019.02.010
- year: 2019
- mesh: Animals, Anti-Bacterial Agents/*pharmacology, Ants, Cell Survival, Cells, Cultured, DNA, Bacterial/genetics, Escherichia coli/drug effects/*growth & development, Fibroblasts/*cytology/drug effects, Humans, Lung Neoplasms/drug therapy/*pathology, Phylogeny, Quinolones/pharmacology, RNA, Ribosomal, 16S/genetics, Streptomyces/isolation & purification/*metabolism
- topic2: Phylogeny
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
9245 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40181) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-40181 | |||
19419 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM40181.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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
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/ | ||||
68368 | Automatically annotated from API 20E | |||||
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 | |||
85147 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID45813.1 | StrainInfo: A central database for resolving microbial strain identifiers |