Strain identifier
BacDive ID: 15448
Type strain: 
Species: Streptomyces olivochromogenes
Strain history: KCC S-0163 <-- IFO 3178 <-- ATCC 3336 <-- S. A. Waksman.
NCBI tax ID(s): 1963 (species)
version 9.1 (current version)
General
@ref: 9552
BacDive-ID: 15448
DSM-Number: 40451
keywords: genome sequence, 16S sequence, Bacteria, spore-forming
description: Streptomyces olivochromogenes DSM 40451 is a spore-forming bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 1963
- Matching level: species
strain history
| @ref | history |
|---|---|
| 9552 | <- E.B. Shirling, ISP <- ATCC <- S.A. Waksman, IMRU |
| 67770 | KCC S-0163 <-- IFO 3178 <-- ATCC 3336 <-- S. A. Waksman. |
doi: 10.13145/bacdive15448.20240916.9.1
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 olivochromogenes
- full scientific name: Streptomyces olivochromogenes (Waksman 1923) Waksman and Henrici 1948 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Actinomyces olivochromogenus
@ref: 9552
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces olivochromogenes
full scientific name: Streptomyces olivochromogenes (Waksman 1923) Waksman and Henrici 1948 emend. Nouioui et al. 2018
type strain: yes
Morphology
colony morphology
| @ref | colony color | incubation period | medium used |
|---|---|---|---|
| 19457 | Beige | 10-14 days | ISP 2 |
| 19457 | Beige | 10-14 days | ISP 3 |
| 19457 | Beige | 10-14 days | ISP 4 |
| 19457 | Beige | 10-14 days | ISP 5 |
| 19457 | Beige | 10-14 days | ISP 6 |
| 19457 | Beige | 10-14 days | ISP 7 |
multicellular morphology
| @ref | forms multicellular complex | medium name |
|---|---|---|
| 19457 | no | ISP 2 |
| 19457 | no | ISP 3 |
| 19457 | no | ISP 4 |
| 19457 | no | ISP 5 |
| 19457 | no | ISP 6 |
| 19457 | no | ISP 7 |
multimedia
- @ref: 9552
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40451.jpg
- caption: Medium 65 28°C
- intellectual property rights: Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 9552 | 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 |
| 19457 | 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 | |
| 19457 | 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: | |
| 19457 | 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 | |
| 19457 | 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 | |
| 19457 | 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 | |
| 19457 | 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 | |
| 9552 | ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 19457 | positive | optimum | 28 |
| 9552 | positive | growth | 28 |
| 67770 | positive | growth | 28 |
Physiology and metabolism
oxygen tolerance
- @ref: 69480
- oxygen tolerance: aerobe
- confidence: 90.787
spore formation
- @ref: 69481
- spore formation: yes
- confidence: 100
compound production
- @ref: 20216
- compound: Streptomycin
halophily
- @ref: 19457
- salt: NaCl
- growth: positive
- tested relation: maximum
- concentration: 2.5 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 19457 | 62968 | cellulose | - | |
| 19457 | 16634 | raffinose | - | |
| 19457 | 26546 | rhamnose | + | |
| 19457 | 28757 | fructose | + | |
| 19457 | 29864 | mannitol | + | |
| 19457 | 17268 | myo-inositol | + | |
| 19457 | 18222 | xylose | - | |
| 19457 | 17992 | sucrose | + | |
| 19457 | 22599 | arabinose | + | |
| 19457 | 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 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 19457 | - | - | - | - | - | - | - | - | - | + | + |
Isolation, sampling and environmental information
isolation
- @ref: 9552
- sample type: soil
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 9552 | 1 | Risk group (German classification) |
| 19457 | 1 | Risk group (German classification) |
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Streptomyces olivochromogenes DSM 40451 16S ribosomal RNA gene, partial sequence | AY094370 | 1448 | nuccore | 1963 |
| 20218 | Streptomyces olivochromogenes gene for 16S ribosomal RNA, partial sequence, strain: JCM 4500 | D44192 | 120 | nuccore | 1963 |
| 20218 | Streptomyces olivochromogenes gene for 16S rRNA, partial sequence, strain: NBRC 13067 | AB184289 | 1470 | nuccore | 1963 |
| 20218 | Streptomyces olivochromogenes gene for 16S rRNA, partial sequence, strain: NBRC 3178 | AB184737 | 1471 | nuccore | 1963 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Streptomyces olivochromogenes strain DSM 40451 | 1963.3 | wgs | patric | 1963 |
| 66792 | Streptomyces olivochromogenes DSM 40451 | 2775507097 | draft | img | 1963 |
| 67770 | Streptomyces olivochromogenes DSM 40451 | GCA_001514115 | scaffold | ncbi | 1963 |
GC content
- @ref: 67770
- GC-content: 70.2
- 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 | 89.061 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 95.066 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 88.928 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 90.787 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 97.5 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 86.5 | no |
External links
@ref: 9552
culture collection no.: DSM 40451, ATCC 25479, ATCC 3336, CBS 889.69, ETH 11886, ETH 14310, ETH 9517, IFO 13067, IMRU 3336, ISP 5451, KCC S-0163, KCC S-0500, NBRC 13067, NRRL B-1341, RIA 1259, JCM 4163, BCRC 15163, CGMCC 4.2000, IFO 3178, IMET 40352, JCM 4500, KCTC 9064, NBRC 3178
straininfo link
- @ref: 84536
- straininfo: 389312
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 15803387 | Streptomyces roseoalbus sp. nov., an actinomycete isolated from soil in Yunnan, China. | Xu LH, Jiang Y, Li WJ, Wen ML, Li MG, Jiang CL | Antonie Van Leeuwenhoek | 10.1007/s10482-004-3720-y | 2005 | Bacterial Typing Techniques, Base Sequence, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Molecular Sequence Data, Phospholipids/analysis/isolation & purification, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Streptomyces/*classification/genetics/*isolation & purification, Vitamin K 2/analysis/isolation & purification | Enzymology |
| Phylogeny | 26790712 | Streptomyces arcticus sp. nov., isolated from frozen soil. | Zhang L, Ruan C, Peng F, Deng Z, Hong K | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000907 | 2016 | ||
| Phylogeny | 27298302 | Streptomyces rhizosphaerihabitans sp. nov. and Streptomyces adustus sp. nov., isolated from bamboo forest soil. | Lee HJ, Whang KS | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001236 | 2016 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sasa/*microbiology, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
| Phylogeny | 33180018 | Steptomyces fagopyri sp. nov., a novel actinomycete isolated from rhizospheric soil of Fagopyrum dibotrys. | Guo Y, Tang X, Hu S, Li K, Zhou M, Jian G | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004555 | 2020 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fagopyrum/*microbiology, Fatty Acids/chemistry, Genome Size, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/isolation & purification, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 9552 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40451) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-40451 | |||
| 19457 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM40451.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 | |||
| 20216 | Curators of the HKI | http://www.leibniz-hki.de/de/ | Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI) | |||
| 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) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 84536 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID389312.1 | StrainInfo: A central database for resolving microbial strain identifiers |