Strain identifier
BacDive ID: 15436
Type strain: 
Species: Streptomyces olivaceus
Strain history: KCC S-0402 <-- IFO 12805 <-- SAJ <-- ISP 5072 <-- IMRU 3335.
NCBI tax ID(s): 47716 (species)
version 8.1 (current version)
General
@ref: 9270
BacDive-ID: 15436
DSM-Number: 40072
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic
description: Streptomyces olivaceus DSM 40072 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.
NCBI tax id
- NCBI tax id: 47716
- Matching level: species
strain history
| @ref | history |
|---|---|
| 9270 | <- E.B. Shirling, ISP <- S.A. Waksman, IMRU |
| 67770 | KCC S-0402 <-- IFO 12805 <-- SAJ <-- ISP 5072 <-- IMRU 3335. |
doi: 10.13145/bacdive15436.20230509.8.1
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 olivaceus
- full scientific name: Streptomyces olivaceus (Waksman 1923) Waksman and Henrici 1948 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Actinomyces olivaceus
@ref: 9270
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces olivaceus
full scientific name: Streptomyces olivaceus (Waksman 1923) Waksman and Henrici 1948 emend. Nouioui et al. 2018
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 93.992 | |
| 69480 | 100 | positive |
colony morphology
| @ref | colony color | incubation period | medium used |
|---|---|---|---|
| 19398 | Yellow | 10-14 days | ISP 2 |
| 19398 | Ivory | 10-14 days | ISP 3 |
| 19398 | Ivory | 10-14 days | ISP 4 |
| 19398 | Yellow | 10-14 days | ISP 5 |
| 19398 | Ivory | 10-14 days | ISP 6 |
| 19398 | Ivory | 10-14 days | ISP 7 |
multicellular morphology
| @ref | forms multicellular complex | complex name | complex color | medium name |
|---|---|---|---|---|
| 19398 | yes | Aerial Mycelium | Yellow | ISP 2 |
| 19398 | yes | Aerial Mycelium | White | ISP 3 |
| 19398 | yes | Aerial Mycelium | Yellow | ISP 4 |
| 19398 | yes | Aerial Mycelium | Grey | ISP 5 |
| 19398 | yes | Aerial Mycelium | Grey | ISP 6 |
| 19398 | yes | Aerial Mycelium | Grey | ISP 7 |
multimedia
- @ref: 9270
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40072.jpg
- caption: Medium 65 37°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 9270 | 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 |
| 19398 | 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 | |
| 19398 | 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: | |
| 19398 | 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 | |
| 19398 | 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 | |
| 19398 | 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 | |
| 19398 | 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 | |
| 9270 | STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) | yes | https://mediadive.dsmz.de/medium/252 | Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 19398 | positive | optimum | 30 | mesophilic |
| 9270 | positive | growth | 37 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore description | spore formation | confidence |
|---|---|---|---|
| 19398 | Formation of spore chains: rectiflixibilis, spore surface: smooth | yes | |
| 69481 | yes | 100 | |
| 69480 | yes | 100 |
compound production
- @ref: 9270
- compound: olivacein
halophily
- @ref: 19398
- salt: NaCl
- growth: positive
- tested relation: maximum
- concentration: 2.5 %
observation
- @ref: 67770
- observation: quinones: MK-9(H6), MK-9(H8)
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 19398 | 62968 | cellulose | - | |
| 19398 | 16634 | raffinose | + | |
| 19398 | 26546 | rhamnose | - | |
| 19398 | 28757 | fructose | + | |
| 19398 | 29864 | mannitol | - | |
| 19398 | 17268 | myo-inositol | - | |
| 19398 | 18222 | xylose | - | |
| 19398 | 17992 | sucrose | + | |
| 19398 | 22599 | arabinose | + | |
| 19398 | 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 | no |
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 19398 | + | - | - | - | - | - | - | - | - | - | + |
Isolation, sampling and environmental information
isolation
- @ref: 9270
- sample type: soil
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 9270 | 1 | Risk group (German classification) |
| 19398 | 1 | Risk group (German classification) |
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Streptomyces olivaceus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4402 | D44117 | 121 | ena | 47716 |
| 20218 | Streptomyces olivaceus gene for 16S rRNA, partial sequence, strain: NBRC 12805 | AB249920 | 1454 | ena | 47716 |
| 20218 | Streptomyces olivaceus gene for 16S rRNA, partial sequence, strain: NBRC 3200 | AB184743 | 1480 | ena | 47716 |
| 20218 | Streptomyces olivaceus strain NRRL B-1224 16S ribosomal RNA gene, partial sequence | EF178681 | 1513 | ena | 47716 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Streptomyces olivaceus CGMCC 4.1369 | GCA_020092305 | contig | ncbi | 47716 |
| 66792 | Streptomyces olivaceus strain CGMCC 4.1369 | 47716.29 | wgs | patric | 47716 |
| 67770 | Streptomyces olivaceus NRRL B-3009 | GCA_000721235 | contig | ncbi | 47716 |
GC content
- @ref: 67770
- GC-content: 72.4
- method: genome sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| gram-positive | yes | 90.998 | no |
| anaerobic | no | 99.078 | no |
| halophile | no | 86.771 | no |
| spore-forming | yes | 95.884 | yes |
| glucose-util | yes | 88.88 | no |
| aerobic | yes | 94.475 | no |
| flagellated | no | 97.709 | no |
| thermophile | no | 99.142 | no |
| motile | no | 94.309 | no |
| glucose-ferment | no | 90.229 | no |
External links
@ref: 9270
culture collection no.: DSM 40072, AS 4.1369, ATCC 19794, ATCC 3335, CBS 281.30, CBS 546.68, CUB 508, ETH 14308, IFO 12805, IMRU 3335, ISP 5072, JCM 4402, KCC S-0402, NBRC 12805, RIA 1073, BCRC 11485, BCRC 12491, CCM 3188, CCUG 11111, CGMCC 4.1336, CGMCC 4.1369, INA 3200, MTCC 1392, NBIMCC 3385, NRRL B-1224, NRRL B-3009, RIA 481, VKM Ac-254, VTT E-073025
straininfo link
- @ref: 84523
- straininfo: 389356
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 20154329 | Streptomyces hyderabadensis sp. nov., an actinomycete isolated from soil. | Reddy TVK, Mahmood S, Paris L, Reddy YHK, Wellington EMH, Idris MM | Int J Syst Evol Microbiol | 10.1099/ijs.0.020446-0 | 2010 | Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/*isolation & purification/physiology | Genetics |
| Metabolism | 31568727 | O-Methyltransferase-Mediated Incorporation of a beta-Amino Acid in Lanthipeptides. | Acedo JZ, Bothwell IR, An L, Trouth A, Frazier C, van der Donk WA | J Am Chem Soc | 10.1021/jacs.9b07396 | 2019 | Alanine/*analogs & derivatives/chemistry, Amino Acid Sequence, *Biocatalysis, Imides/chemistry, Methyltransferases/chemistry/*metabolism, Models, Molecular, Peptides/*chemistry, Protein Conformation, Streptomyces/enzymology, Sulfides/*chemistry | Enzymology |
| 31750037 | An "olivomycin A" derivative from a sponge-associated Streptomyces sp. strain SP 85. | Gozari M, Bahador N, Mortazavi MS, Eftekhar E, Jassbi AR | 3 Biotech | 10.1007/s13205-019-1964-5 | 2019 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 9270 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40072) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-40072 | |||
| 19398 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM40072.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 | |||
| 84523 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID389356.1 | StrainInfo: A central database for resolving microbial strain identifiers |