Strain identifier
BacDive ID: 16210
Type strain: 
Species: Streptomyces variegatus
Strain history: VKM Ac-141 <-- INMI 702.
NCBI tax ID(s): 284031 (species)
version 9.1 (current version)
General
@ref: 10343
BacDive-ID: 16210
DSM-Number: 41479
keywords: genome sequence, 16S sequence, Bacteria, spore-forming
description: Streptomyces variegatus DSM 41479 is a spore-forming bacterium that builds an aerial mycelium and was isolated from soil.
NCBI tax id
- NCBI tax id: 284031
- Matching level: species
strain history
| @ref | history |
|---|---|
| 10343 | <- N. S. Agre, VKM |
| 67770 | VKM Ac-141 <-- INMI 702. |
doi: 10.13145/bacdive16210.20240916.9.1
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 variegatus
- full scientific name: Streptomyces variegatus Sveshnikova and Timuk 1986
synonyms
- @ref: 20215
- synonym: Streptomyces flavovariabilis
@ref: 10343
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces flavovariabilis
full scientific name: Streptomyces flavovariabilis (ex Korenyako and Nikitina 1965) Sveshnikova 1986 emend. Nouioui et al. 2018
type strain: yes
Morphology
colony morphology
| @ref | colony color | incubation period | medium used |
|---|---|---|---|
| 18697 | Bottle green (6007) | 10-14 days | ISP 2 |
| 18697 | Green | 10-14 days | ISP 3 |
| 18697 | Colorless | 10-14 days | ISP 4 |
| 18697 | Colorless | 10-14 days | ISP 5 |
| 18697 | Brown | 10-14 days | ISP 6 |
| 18697 | Colorless | 10-14 days | ISP 7 |
multicellular morphology
| @ref | forms multicellular complex | complex name | complex color | medium name |
|---|---|---|---|---|
| 18697 | yes | Aerial Mycelium | White | ISP 2 |
| 18697 | yes | Aerial Mycelium | White | ISP 3 |
| 18697 | yes | Aerial Mycelium | Sparse, white | ISP 4 |
| 18697 | yes | Aerial Mycelium | White | ISP 5 |
| 18697 | no | ISP 6 | ||
| 18697 | no | ISP 7 |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 10343 | 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 |
| 18697 | 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 | |
| 18697 | 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: | |
| 18697 | 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 | |
| 18697 | 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 | |
| 18697 | 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 | |
| 18697 | 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 |
|---|---|---|---|
| 10343 | positive | growth | 28 |
| 18697 | positive | optimum | 28 |
| 67770 | positive | growth | 28 |
Physiology and metabolism
oxygen tolerance
- @ref: 69480
- oxygen tolerance: aerobe
- confidence: 90.254
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69480 | yes | 91.913 |
| 69481 | yes | 100 |
halophily
- @ref: 18697
- salt: NaCl
- growth: positive
- tested relation: maximum
- concentration: 7.5 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 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 | no |
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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 18697 | + | + | + | + | + | - | + | - | - | + | + |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 10343 | soil | Sibiria, Taiga | Russia | RUS | Asia |
| 67770 | Soil | Russia | RUS |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 10343 | 1 | Risk group (German classification) |
| 18697 | 1 | German classification |
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Streptomyces flavovariabilis 16S rRNA gene, type strain LMG 19905 | AJ781334 | 1478 | nuccore | 284031 |
| 20218 | Streptomyces flavovariabilis gene for 16S rRNA, partial sequence, strain: NBRC 100764 | AB249931 | 1481 | nuccore | 284031 |
| 20218 | Streptomyces flavovariabilis strain NRRL B-16367 16S ribosomal RNA gene, partial sequence | EF178691 | 1496 | nuccore | 284031 |
Genome sequences
- @ref: 67770
- description: Streptomyces flavovariabilis NRRL B-16367
- accession: GCA_000725785
- assembly level: scaffold
- database: ncbi
- NCBI tax ID: 284031
GC content
- @ref: 67770
- GC-content: 71.2
- method: genome sequence analysis
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 89.352 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 96.04 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 90.254 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 91.913 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 97 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 87.5 | no |
External links
@ref: 10343
culture collection no.: DSM 41479, ATCC 43684, DSM 41503, DSM 41688, INMI 702, NRRL B-16367, VKM Ac-141, JCM 9089, CGMCC 4.1942, NBRC 100764
straininfo link
- @ref: 85271
- straininfo: 46063
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 27752797 | Streptomyces luozhongensis sp. nov., a novel actinomycete with antifungal activity and antibacterial activity. | Zhang R, Han X, Xia Z, Luo X, Wan C, Zhang L | Antonie Van Leeuwenhoek | 10.1007/s10482-016-0790-6 | 2016 | Anti-Bacterial Agents/classification/metabolism, Antifungal Agents/classification/metabolism, Bacteria, Base Composition/genetics, DNA, Bacterial/genetics, Fungi/growth & development, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Species Specificity, Streptomyces/*classification/genetics/metabolism/*physiology | Metabolism |
| Phylogeny | 30026482 | Streptomyces qaidamensis sp. nov., isolated from sand in the Qaidam Basin, China. | Zhang B, Tang S, Chen X, Zhang G, Zhang W, Chen T, Liu G, Li S, Dos Santos LT, Castro HC, Facey P, Hitchings M, Dyson P | J Antibiot (Tokyo) | 10.1038/s41429-018-0080-9 | 2018 | China, Genome, Bacterial, Phylogeny, *Soil Microbiology, Streptomyces/*classification/*genetics/isolation & purification/ultrastructure | Genetics |
| Phylogeny | 32176603 | Streptomyces cahuitamycinicus sp. nov., isolated from desert soil and reclassification of Streptomyces galilaeus as a later heterotypic synonym of Streptomyces bobili. | Saygin H, Ay H, Guven K, Cetin D, Sahin N | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004103 | 2020 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Desert Climate, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Genes, Bacterial, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/isolation & purification, Turkmenistan, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 10343 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 41479) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-41479 | |||
| 18697 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM41479.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 | |
| 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 | |||
| 85271 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID46063.1 | StrainInfo: A central database for resolving microbial strain identifiers |