Strain identifier
BacDive ID: 15130
Type strain: 
Species: Streptomyces echinatus
Strain history: KCC S-0144 <-- Y. Okami (NIHJ 180) <-- ETH 8331.
NCBI tax ID(s): 67293 (species)
version 8.1 (current version)
General
@ref: 9214
BacDive-ID: 15130
DSM-Number: 40013
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, antibiotic compound production
description: Streptomyces echinatus DSM 40013 is a spore-forming, mesophilic bacterium that produces antibiotic compounds and was isolated from soil.
NCBI tax id
- NCBI tax id: 67293
- Matching level: species
strain history
| @ref | history |
|---|---|
| 9214 | <- E.B. Shirling, ISP <- R. Hütter, ETH |
| 67770 | KCC S-0144 <-- Y. Okami (NIHJ 180) <-- ETH 8331. |
doi: 10.13145/bacdive15130.20230509.8.1
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 echinatus
- full scientific name: Streptomyces echinatus Corbaz et al. 1957 (Approved Lists 1980)
@ref: 9214
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces echinatus
full scientific name: Streptomyces echinatus Corbaz et al. 1957
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 92.433 | |
| 69480 | 100 | positive |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 9214 | 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 |
| 9214 | 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 |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 9214 | 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 |
|---|---|
| 9214 | echinomycin (= levomycin, echanomycin, guinomycin A) |
| 20216 | Echinomycin |
| 20216 | Glukoseisomerase |
metabolite production
- @ref: 67770
- Chebi-ID: 80052
- metabolite: echinomycin
- production: yes
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent |
|---|---|---|---|---|
| 9214 | soil | Angola | AGO | Africa |
| 67770 | Soil | Angola | AGO | Africa |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
- @ref: 9214
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Streptomyces echinatus partial 16S rRNA gene, strain ISP 5013 | AJ399465 | 1448 | ena | 67293 |
| 20218 | Streptomyces echinatus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4574 | D44242 | 120 | ena | 67293 |
| 20218 | Streptomyces echinatus gene for 16S rRNA, partial sequence, strain: NBRC 12763 | AB184126 | 1438 | ena | 67293 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Streptomyces echinatus CECT 3313 | GCA_014203595 | scaffold | ncbi | 67293 |
| 66792 | Streptomyces echinatus JCM4574 | GCA_020400685 | contig | ncbi | 67293 |
| 66792 | Streptomyces echinatus strain CECT 3313 | 67293.4 | wgs | patric | 67293 |
| 66792 | Streptomyces echinatus CECT 3313 | 2863298641 | draft | img | 67293 |
GC content
- @ref: 67770
- GC-content: 72.3
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| flagellated | no | 98.264 | no |
| gram-positive | yes | 88.459 | no |
| anaerobic | no | 99.233 | no |
| aerobic | yes | 93.498 | no |
| halophile | no | 94.885 | no |
| spore-forming | yes | 94.225 | no |
| glucose-util | yes | 88.561 | no |
| thermophile | no | 98.439 | yes |
| motile | no | 93.826 | no |
| glucose-ferment | no | 88.892 | no |
External links
@ref: 9214
culture collection no.: DSM 40013, ATCC 19748, CBS 409.59, CBS 487.68, CUB 95, DSM 41251, ETH 8331, IFO 12763, ISP 5013, JCM 4144, JCM 4574, KCC S-0144, KCC S-0574, NBRC 12763, NRRL 2587, RIA 1029, ATCC 21133, BCRC 13656, CBS 684.73, CECT 3313, CGMCC 4.1642, HUT 6090, IFM 1076, IMET 40461, KCTC 9724, LMG 5972, NCIMB 9598, NCIMB 9799, VKM Ac-762
straininfo link
- @ref: 84235
- straininfo: 92443
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 26510888 | Streptomyces actinomycinicus sp. nov., isolated from soil of a peat swamp forest. | Tanasupawat S, Phongsopitanun W, Suwanborirux K, Ohkuma M, Kudo T | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000716 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification, Thailand, Vitamin K 2/analogs & derivatives/chemistry, *Wetlands | Genetics |
| Phylogeny | 27826672 | Streptomyces xiangtanensis sp. nov., isolated from a manganese-contaminated soil. | Mo P, Yu YZ, Zhao JR, Gao J | Antonie Van Leeuwenhoek | 10.1007/s10482-016-0797-z | 2016 | Cell Wall/chemistry, China, Manganese/*chemistry, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sodium Chloride/metabolism, Soil/chemistry, *Soil Microbiology, Soil Pollutants/*chemistry, Species Specificity, Streptomyces/*classification/genetics/*isolation & purification/physiology | Phenotype |
| Phylogeny | 34196604 | Streptomyces musisoli sp. nov., an actinomycete isolated from soil. | Duangupama T, Intaraudom C, Pittayakhajonwut P, Suriyachadkun C, Tadtong S, Sirirote P, Tanasupawat S, Thawai C | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004857 | 2021 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Musa, Mycelium, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/isolation & purification, Thailand, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 9214 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40013) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-40013 | |||
| 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/ | ||||
| 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 | |||
| 84235 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID92443.1 | StrainInfo: A central database for resolving microbial strain identifiers |