Strain identifier
BacDive ID: 16061
Type strain: 
Species: Streptomyces umbrinus
Strain history: KCC S-0521 <-- IFO 13091 <-- SAJ <-- ISP 5278 <-- INA 1703/53.
NCBI tax ID(s): 67370 (species)
version 9.1 (current version)
General
@ref: 9429
BacDive-ID: 16061
DSM-Number: 40278
keywords: genome sequence, 16S sequence, Bacteria, spore-forming
description: Streptomyces umbrinus DSM 40278 is a spore-forming bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 67370
- Matching level: species
strain history
| @ref | history |
|---|---|
| 9429 | <- E.B. Shirling, ISP <- G.F. Gauze INA |
| 67770 | KCC S-0521 <-- IFO 13091 <-- SAJ <-- ISP 5278 <-- INA 1703/53. |
doi: 10.13145/bacdive16061.20240916.9.1
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 umbrinus
- full scientific name: Streptomyces umbrinus (Sveshnikova 1957) Pridham et al. 1958 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Actinomyces umbrinus
@ref: 9429
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces umbrinus
full scientific name: Streptomyces umbrinus (Sveshnikova 1957) Pridham et al. 1958
type strain: yes
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 9429 | 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 |
| 9429 | ISP 5 MEDIUM (DSMZ Medium 993) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium993.pdf |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 9429 | positive | growth | 28 |
| 67770 | positive | growth | 28 |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69480 | yes | 93.486 |
| 69481 | yes | 100 |
observation
- @ref: 67770
- observation: quinones: MK-9(H6), MK-9(H8)
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | continent | origin.country |
|---|---|---|---|---|
| 9429 | soil | USSR | Asia | |
| 67770 | Soil | Russia | RUS |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
Safety information
risk assessment
- @ref: 9429
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Streptomyces umbrinus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4521 | D44209 | 120 | nuccore | 67370 |
| 20218 | Streptomyces umbrinus gene for 16S rRNA, partial sequence, strain: NBRC 13091 | AB184305 | 1479 | nuccore | 67370 |
| 20218 | Streptomyces umbrinus strain NRRL B-2572T 16S ribosomal RNA gene, partial sequence | DQ442549 | 1538 | nuccore | 67370 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Streptomyces umbrinus strain JCM 4521 | 67370.3 | wgs | patric | 67370 |
| 67770 | Streptomyces umbrinus JCM 4521 | GCA_014650195 | scaffold | ncbi | 67370 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 88.11 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 96.473 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | yes | 93.486 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 87.562 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 96.5 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 88 | no |
External links
@ref: 9429
culture collection no.: DSM 40278, ATCC 19929, ATCC 25503, CBS 645.69, IFO 13091, INA 1703, ISP 5278, NBRC 13091, RIA 1283, JCM 4521, BCRC 15129, CGMCC 4.1791, INA 1703/53, NRRL B-2572, VKM Ac-1747
straininfo link
- @ref: 85134
- straininfo: 389294
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 28382471 | Two new species of the genus Streptomyces: Streptomyces camponoti sp. nov. and Streptomyces cuticulae sp. nov. isolated from the cuticle of Camponotus japonicus Mayr. | Piao C, Zheng W, Li Y, Liu C, Jin L, Song W, Yan K, Wang X, Xiang W | Arch Microbiol | 10.1007/s00203-017-1353-6 | 2017 | Animals, Ants/*microbiology, Bacterial Typing Techniques, China, DNA Gyrase/genetics, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Streptomyces/classification/genetics/isolation & purification | Transcriptome |
| Phylogeny | 35471105 | Streptomyces liliifuscus sp. nov and an anti-ginger plague agent Streptomyces liliiviolaceus sp. nov, two novel species isolated from soil of Lilium lancifolium. | Li K, Man Y, Liu J, Liu Z, Ma H, Zhu H, Zhou Y, Zhang C, Zhou X | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005340 | 2022 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Ginger/genetics, *Lilium/genetics, Phylogeny, *Plague, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Soil Microbiology, *Streptomyces | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 9429 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40278) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-40278 | |||
| 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/ | ||||
| 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 | |||
| 85134 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID389294.1 | StrainInfo: A central database for resolving microbial strain identifiers |