Strain identifier
BacDive ID: 15451
Type strain: 
Species: Streptomyces omiyaensis
Strain history: KCC S-0806 <-- IFO 13449 <-- SAJ <-- ISP 5552 <-- NRRL B-1587 <-- Y. Okami (NIHJ 102).
NCBI tax ID(s): 68247 (species)
version 8.1 (current version)
General
@ref: 9635
BacDive-ID: 15451
DSM-Number: 40552
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, antibiotic compound production
description: Streptomyces omiyaensis DSM 40552 is a spore-forming, mesophilic bacterium that produces antibiotic compounds and was isolated from soil.
NCBI tax id
- NCBI tax id: 68247
- Matching level: species
strain history
| @ref | history |
|---|---|
| 9635 | <- E.B. Shirling, ISP <- NRRL <- Umezawa, NIHJ |
| 67770 | KCC S-0806 <-- IFO 13449 <-- SAJ <-- ISP 5552 <-- NRRL B-1587 <-- Y. Okami (NIHJ 102). |
doi: 10.13145/bacdive15451.20230509.8.1
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 omiyaensis
- full scientific name: Streptomyces omiyaensis Umezawa and Okami 1950 (Approved Lists 1980)
@ref: 9635
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces omiyaensis
full scientific name: Streptomyces omiyaensis Umezawa and Okami 1950
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 96.789 | |
| 69480 | 100 | positive |
Culture and growth conditions
culture medium
- @ref: 9635
- name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
- growth: yes
- link: https://mediadive.dsmz.de/medium/65
- composition: 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
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 9635 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 100 |
compound production
| @ref | compound |
|---|---|
| 9635 | chloramphenicol |
| 20216 | Chloramphenicol |
metabolite production
- @ref: 67770
- Chebi-ID: 17698
- metabolite: chloramphenicol
- production: yes
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent | geographic location |
|---|---|---|---|---|---|
| 9635 | soil | Japan | JPN | Asia | |
| 67770 | Soil | Japan | JPN | Asia | Omiya, Saitama Pref. |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_490.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_109;98_403;99_490&stattab=map
- Last taxonomy: Streptomyces
- 16S sequence: EF178697
- Sequence Identity:
- Total samples: 9252
- soil counts: 6254
- aquatic counts: 336
- animal counts: 471
- plant counts: 2191
Safety information
risk assessment
- @ref: 9635
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Streptomyces omiyaensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 4806 | D44376 | 120 | ena | 68247 |
| 20218 | Streptomyces omiyaensis gene for 16S rRNA, partial sequence, strain: NBRC 13449 | AB184411 | 1467 | ena | 68247 |
| 20218 | Streptomyces omiyaensis strain NRRL B-1587 16S ribosomal RNA gene, partial sequence | EF178697 | 1482 | ena | 68247 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Streptomyces omiyaensis JCM 4806 | GCA_014650895 | scaffold | ncbi | 68247 |
| 66792 | Streptomyces omiyaensis strain JCM 4806 | 68247.3 | wgs | patric | 68247 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| flagellated | no | 97.701 | no |
| gram-positive | yes | 87.844 | no |
| anaerobic | no | 99.193 | no |
| aerobic | yes | 92.349 | no |
| halophile | no | 91.568 | no |
| spore-forming | yes | 93.294 | no |
| thermophile | no | 99.129 | yes |
| glucose-util | yes | 88.417 | no |
| motile | no | 92.227 | no |
| glucose-ferment | no | 86.471 | no |
External links
@ref: 9635
culture collection no.: DSM 40552, ATCC 27454, CBS 750.72, IFO 13449, ISP 5552, JCM 4806, NBRC 13449, NRRL B-1587, RIA 1410, NIHJ 102, BCRC 11897, CGMCC 4.1987, IMET 43362, VKM Ac-1903
straininfo link
- @ref: 84539
- straininfo: 297033
literature
- topic: Phylogeny
- Pubmed-ID: 27330275
- title: Isolation and characterization of cyclo-(tryptophanyl-prolyl) and chloramphenicol from Streptomyces sp. SUK 25 with antimethicillin-resistant Staphylococcus aureus activity.
- authors: Alshaibani MM, Jalil J, Sidik NM, Edrada-Ebel R, Zin NM
- journal: Drug Des Devel Ther
- DOI: 10.2147/DDDT.S101212
- year: 2016
- mesh: Anti-Bacterial Agents/chemistry/*pharmacology, Anti-Infective Agents/chemistry/*pharmacology, Chloramphenicol/chemistry/*isolation & purification/*pharmacology, Methicillin-Resistant Staphylococcus aureus/drug effects, RNA, Ribosomal, 16S/chemistry/*genetics, Tryptophan/*analogs & derivatives/chemistry/isolation & purification/pharmacology
- topic2: Enzymology
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 9635 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40552) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-40552 | |||
| 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) | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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 | |||
| 84539 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297033.1 | StrainInfo: A central database for resolving microbial strain identifiers |