Strain identifier
BacDive ID: 16313
Type strain: 
Species: Streptomyces nojiriensis
Strain history: Meiji Seika Kaisha, Ltd.; SF-426.
NCBI tax ID(s): 66374 (species)
version 8.1 (current version)
General
@ref: 10431
BacDive-ID: 16313
DSM-Number: 41655
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, antibiotic compound production
description: Streptomyces nojiriensis DSM 41655 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and produces antibiotic compounds.
NCBI tax id
- NCBI tax id: 66374
- Matching level: species
strain history
| @ref | history |
|---|---|
| 10431 | <- IFO <- Meiji Seika Kaisha, Ltd., T. Shomura, SF-426 |
| 67770 | Meiji Seika Kaisha, Ltd.; SF-426. |
doi: 10.13145/bacdive16313.20230509.8.1
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 nojiriensis
- full scientific name: Streptomyces nojiriensis Ishida et al. 1967 (Approved Lists 1980)
@ref: 10431
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces nojiriensis
full scientific name: Streptomyces nojiriensis Ishida et al. 1967
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 93.265 | |
| 69480 | 100 | positive |
colony morphology
| @ref | colony color | incubation period | medium used |
|---|---|---|---|
| 18700 | Beige | 10-14 days | ISP 2 |
| 18700 | Beige | 10-14 days | ISP 3 |
| 18700 | Beige | 10-14 days | ISP 4 |
| 18700 | Beige | 10-14 days | ISP 5 |
| 18700 | Brown | 10-14 days | ISP 6 |
| 18700 | Brown | 10-14 days | ISP 7 |
multicellular morphology
| @ref | forms multicellular complex | complex name | complex color | medium name |
|---|---|---|---|---|
| 18700 | yes | Aerial Mycelium | Grey | ISP 2 |
| 18700 | yes | Aerial Mycelium | Grey | ISP 3 |
| 18700 | yes | Aerial Mycelium | Grey | ISP 4 |
| 18700 | yes | Aerial Mycelium | Grey | ISP 5 |
| 18700 | no | ISP 6 | ||
| 18700 | yes | Aerial Mycelium | Grey | ISP 7 |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 10431 | ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) | yes | https://mediadive.dsmz.de/medium/84 | Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water |
| 10431 | 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 |
| 18700 | 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 | |
| 18700 | 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: | |
| 18700 | 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 | |
| 18700 | 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 | |
| 18700 | 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 | |
| 18700 | 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 | |
| 10431 | N-Z-AMINE-MEDIUM (DSMZ Medium 554) | yes | https://mediadive.dsmz.de/medium/554 | Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 10431 | positive | growth | 28 | mesophilic |
| 18700 | positive | optimum | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore description | spore formation | confidence |
|---|---|---|---|
| 18700 | Formation of spore chains (spirales)(sp), spore surface smooth | yes | |
| 69481 | yes | 100 | |
| 69480 | yes | 100 |
compound production
| @ref | compound |
|---|---|
| 10431 | nojirimycin |
| 18700 | Streptothricines |
halophily
- @ref: 18700
- salt: NaCl
- growth: positive
- tested relation: maximum
- concentration: 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 |
|---|---|---|---|
| 67770 | 28945 | nojirimycin | yes |
| 68368 | 15688 | acetoin | no |
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 18700 | - | + | - | - | + | + | + | + | - | - | - |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 10431 | soil | Nagano Pref., Nojiri | Japan | JPN | Asia |
| 67770 | Soil | Nemuro, Hokkaido | Japan | JPN | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_163.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_109;98_144;99_163&stattab=map
- Last taxonomy: Streptomyces
- 16S sequence: AJ781355
- Sequence Identity:
- Total samples: 26399
- soil counts: 19336
- aquatic counts: 1680
- animal counts: 1702
- plant counts: 3681
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 10431 | 1 | Risk group (German classification) |
| 18700 | 1 | German classification |
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Streptomyces nojiriensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 3382 | D43984 | 120 | ena | 66374 |
| 20218 | Streptomyces nojiriensis strain KCTC 9784 16S ribosomal RNA gene, partial sequence | AY999814 | 1419 | ena | 66374 |
| 20218 | Streptomyces nojiriensis 16S rRNA gene, type strain LMG 20094 | AJ781355 | 1477 | ena | 66374 |
| 20218 | Streptomyces nojiriensis gene for 16S rRNA, partial sequence, strain: NBRC 13794 | AB184485 | 1475 | ena | 66374 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Streptomyces nojiriensis JCM 3382 | GCA_017639205 | complete | ncbi | 66374 |
| 66792 | Streptomyces nojiriensis NBRC 13794 | GCA_016755855 | contig | ncbi | 66374 |
| 66792 | Streptomyces nojiriensis JCM 3382 | GCA_014648615 | scaffold | ncbi | 66374 |
| 66792 | Streptomyces nojiriensis strain JCM 3382 | 66374.6 | complete | patric | 66374 |
| 66792 | Streptomyces nojiriensis strain JCM 3382 | 66374.4 | wgs | patric | 66374 |
| 66792 | Streptomyces nojiriensis strain NBRC 13794 | 66374.5 | wgs | patric | 66374 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| flagellated | no | 97.4 | no |
| gram-positive | yes | 86.722 | no |
| anaerobic | no | 99.188 | no |
| aerobic | yes | 89.22 | no |
| halophile | no | 96.248 | no |
| spore-forming | yes | 93.628 | yes |
| thermophile | no | 99.424 | yes |
| glucose-util | yes | 89.52 | no |
| motile | no | 94.44 | no |
| glucose-ferment | no | 88.674 | no |
External links
@ref: 10431
culture collection no.: DSM 41655, ATCC 29781, IFO 13794, JCM 3382, NBRC 13794, NRRL B-16930, CGMCC 4.1897, KCTC 9784
straininfo link
- @ref: 85369
- straininfo: 39716
literature
- Pubmed-ID: 34576698
- title: Genome Analysis of Streptomyces nojiriensis JCM 3382 and Distribution of Gene Clusters for Three Antibiotics and an Azasugar across the Genus Streptomyces.
- authors: Park JS, Kim DE, Hong SC, Kim SY, Kwon HC, Hyun CG, Choi J
- journal: Microorganisms
- DOI: 10.3390/microorganisms9091802
- year: 2021
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 10431 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 41655) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-41655 | |||
| 18700 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM41655.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 | |||||
| 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 | |||
| 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 | |||
| 85369 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID39716.1 | StrainInfo: A central database for resolving microbial strain identifiers |