Strain identifier
BacDive ID: 15049
Type strain: 
Species: Streptomyces bikiniensis
Strain history: KCC S-0011 <-- H. Yonehara (IAM 0019) <-- NRRL B-1049 <-- IMRU 3514.
NCBI tax ID(s): 1896 (species)
version 8.1 (current version)
General
@ref: 9661
BacDive-ID: 15049
DSM-Number: 40581
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, antibiotic compound production
description: Streptomyces bikiniensis DSM 40581 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and produces antibiotic compounds.
NCBI tax id
- NCBI tax id: 1896
- Matching level: species
strain history
| @ref | history |
|---|---|
| 9661 | <- E.B. Shirling, ISP <- ATCC <- IMRU |
| 67770 | KCC S-0011 <-- H. Yonehara (IAM 0019) <-- NRRL B-1049 <-- IMRU 3514. |
doi: 10.13145/bacdive15049.20230509.8.1
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 bikiniensis
- full scientific name: Streptomyces bikiniensis Johnstone and Waksman 1947 (Approved Lists 1980)
@ref: 9661
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces bikiniensis
full scientific name: Streptomyces bikiniensis Johnstone and Waksman 1947 emend. Nouioui et al. 2018
type strain: yes
Morphology
colony morphology
| @ref | colony color | incubation period | medium used |
|---|---|---|---|
| 19478 | Yellow | 10-14 days | ISP 2 |
| 19478 | Yellow - Green | 10-14 days | ISP 3 |
| 19478 | Yellow | 10-14 days | ISP 4 |
| 19478 | Yellow | 10-14 days | ISP 5 |
| 19478 | Yellow | 10-14 days | ISP 6 |
| 19478 | Yellow | 10-14 days | ISP 7 |
multicellular morphology
| @ref | forms multicellular complex | complex name | complex color | medium name |
|---|---|---|---|---|
| 19478 | yes | Aerial Mycelium | Gray | ISP 2 |
| 19478 | yes | Aerial Mycelium | Gray | ISP 3 |
| 19478 | yes | Aerial Mycelium | Gray | ISP 4 |
| 19478 | yes | Aerial Mycelium | Gray | ISP 5 |
| 19478 | no | ISP 6 | ||
| 19478 | yes | Aerial Mycelium | Gray | ISP 7 |
multimedia
- @ref: 9661
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40581.jpg
- caption: Medium 65 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 9661 | 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 |
| 19478 | 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 | |
| 19478 | 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: | |
| 19478 | 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 | |
| 19478 | 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 | |
| 19478 | 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 | |
| 19478 | 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 | |
| 9661 | 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 |
|---|---|---|---|---|
| 19478 | positive | optimum | 28 | mesophilic |
| 9661 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
- @ref: 19478
- spore description: Formation of spore chains (rectiflixibilis), spore surface smooth
- type of spore: spore
- spore formation: yes
compound production
| @ref | compound |
|---|---|
| 9661 | streptomycin II |
| 20216 | Streptomycin |
| 20216 | Glucoseisomerase |
| 19478 | Chalcomycin |
| 67770 | Streptomycin II |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 19478 | 62968 | cellulose | - | |
| 19478 | 16634 | raffinose | - | |
| 19478 | 26546 | rhamnose | - | |
| 19478 | 28757 | fructose | - | |
| 19478 | 29864 | mannitol | - | |
| 19478 | 17268 | myo-inositol | - | |
| 19478 | 18222 | xylose | - | |
| 19478 | 17992 | sucrose | - | |
| 19478 | 22599 | arabinose | - | |
| 19478 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 19478 | + | + | + | + | - | - | + | - | - | - | + |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 9661 | soil | Bikini atoll | USA | USA | North America |
| 67770 | Soil | Bikini Atoll | Marshall Islands | MHL | Australia and Oceania |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_2484.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_109;98_766;99_2484&stattab=map
- Last taxonomy: Streptomyces
- 16S sequence: X79851
- Sequence Identity:
- Total samples: 971
- soil counts: 718
- aquatic counts: 54
- animal counts: 76
- plant counts: 123
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 9661 | 1 | Risk group (German classification) |
| 19478 | 1 | Risk group (German classification) |
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Streptomyces bikiniensis 16S ribosomal RNA gene, partial sequence | U72174 | 269 | ena | 1896 |
| 20218 | Streptomyces bikiniensis 16S rRNA gene, strain DSM40581 | X79851 | 1517 | ena | 1896 |
| 20218 | Streptomyces bikiniensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 4011 | D43987 | 120 | ena | 1896 |
| 20218 | Streptomyces bikiniensis gene for 16S rRNA, partial sequence, strain: NBRC 14598 | AB184602 | 1476 | ena | 1896 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 67770 | Streptomyces bikiniensis NRRL B-1049 | GCA_000716465 | contig | ncbi | 1896 |
| 67770 | Streptomyces bikiniensis NRRL ISP-5581 | GCA_000716245 | scaffold | ncbi | 1896 |
GC content
- @ref: 67770
- GC-content: 73.1
- method: genome sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 95.25 | no |
| flagellated | no | 97.425 | no |
| gram-positive | yes | 90.336 | no |
| anaerobic | no | 99.125 | no |
| halophile | no | 96.118 | no |
| spore-forming | yes | 94.763 | yes |
| thermophile | no | 98.556 | no |
| glucose-util | yes | 90.262 | yes |
| aerobic | yes | 91.56 | no |
| glucose-ferment | no | 88.178 | no |
External links
@ref: 9661
culture collection no.: DSM 40581, ATCC 11062, ETH 14303, IMRU 3514, ISP 5581, JCM 4011, NRRL B-1049, BCRC 15171, CBS 412.54, CGMCC 4.0569, HUT 6084, IFM 1057, IFO 14598, IMET 41362, KCTC 9172, MTCC 1539, NBIMCC 1504, NBRC 14598, NRRL B-2690, NRRL ISP-5581, RIA 471, RIA 74, VKM Ac-999, VTT E-82155
straininfo link
- @ref: 84155
- straininfo: 13365
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 1672125 | Melanostatin, a new melanin synthesis inhibitor. Production, isolation, chemical properties, structure and biological activity. | Ishihara Y, Oka M, Tsunakawa M, Tomita K, Hatori M, Yamamoto H, Kamei H, Miyaki T, Konishi M, Oki T | J Antibiot (Tokyo) | 10.7164/antibiotics.44.25 | 1991 | Chromatography, Thin Layer, Fermentation, MSH Release-Inhibiting Hormone/*biosynthesis/chemistry/isolation & purification/pharmacology, Magnetic Resonance Spectroscopy, Melanins/*antagonists & inhibitors/biosynthesis, Melanoma, Experimental, Microscopy, Electron, Scanning, Molecular Structure, Monophenol Monooxygenase/antagonists & inhibitors, Soil Microbiology, Solubility, Spectrophotometry, Infrared, Streptomyces/*classification/drug effects/metabolism/ultrastructure, Tumor Cells, Cultured | Biotechnology |
| Metabolism | 2126003 | A new screening method for melanin biosynthesis inhibitors using Streptomyces bikiniensis. | Tomita K, Oda N, Ohbayashi M, Kamei H, Miyaki T, Oki T | J Antibiot (Tokyo) | 10.7164/antibiotics.43.1601 | 1990 | Histidine/analogs & derivatives/pharmacology, Melanins/antagonists & inhibitors/*biosynthesis/pharmacology, Melanoma, Experimental/*metabolism, Monophenol Monooxygenase/antagonists & inhibitors, Streptomyces/*drug effects/metabolism, Tetracyclines/pharmacology, Tumor Cells, Cultured, Virginiamycin/pharmacology | Pathogenicity |
| Metabolism | 5808071 | Enzymatic phosphorylation of streptomycin by extracts of streptomycin-producing strains of Streptomyces. | Miller AL, Walker JB | J Bacteriol | 10.1128/jb.99.2.401-405.1969 | 1969 | Adenosine Triphosphate/metabolism, Alkaline Phosphatase/metabolism, Carbon Isotopes, Chromatography, Paper, Phosphorus Isotopes, Phosphotransferases/*metabolism, Streptomyces/enzymology/*metabolism, Streptomycin/*metabolism | Enzymology |
| Phylogeny | 17684254 | Streptomyces vietnamensis sp. nov., a streptomycete with violet blue diffusible pigment isolated from soil in Vietnam. | Zhu HH, Guo J, Yao Q, Yang SZ, Deng MR, Phuong LTB, Hanh VT, Ryan MJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.64774-0 | 2007 | DNA, Bacterial, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, Pigments, Biological/biosynthesis, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Streptomyces/*classification/genetics/*isolation & purification/physiology, Trees, Vietnam | Genetics |
| Phylogeny | 32790603 | Streptomyces apocyni sp. nov., an endogenous actinomycete isolated from Apocynum venetum. | Liu WX, Ma LR, Xia ZF, Zeng H, Luo XX, Zhang LL, Wan CX | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004357 | 2020 | Apocynum/*microbiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptomyces/*classification/isolation & purification, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 9661 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40581) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-40581 | |||
| 19478 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM40581.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 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 68368 | Automatically annotated from API 20E | |||||
| 69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 84155 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID13365.1 | StrainInfo: A central database for resolving microbial strain identifiers |