Strain identifier
BacDive ID: 16625
Type strain: 
Species: Sphaerisporangium rubeum
Strain Designation: 3D-72(35)
Strain history: I. Ara 3D-72(35).
NCBI tax ID(s): 321317 (species)
version 8.1 (current version)
General
@ref: 12105
BacDive-ID: 16625
DSM-Number: 44936
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic
description: Sphaerisporangium rubeum 3D-72 is an aerobe, spore-forming, mesophilic bacterium that was isolated from sandy soil.
NCBI tax id
- NCBI tax id: 321317
- Matching level: species
strain history
| @ref | history |
|---|---|
| 12105 | <- T. Kudo, JCM (Sphaerosporangium rubeum) <- I. Ara; 3D-72(35) |
| 67770 | I. Ara 3D-72(35). |
doi: 10.13145/bacdive16625.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Streptosporangiales
- family: Streptosporangiaceae
- genus: Sphaerisporangium
- species: Sphaerisporangium rubeum
- full scientific name: Sphaerisporangium rubeum corrig. Ara and Kudo 2007
synonyms
- @ref: 20215
- synonym: Sphaerosporangium rubeum
@ref: 12105
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptosporangiaceae
genus: Sphaerisporangium
species: Sphaerisporangium rubeum
full scientific name: Sphaerisporangium rubeum Ara and Kudo 2007
strain designation: 3D-72(35)
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 94.703 | |
| 69480 | 100 | positive |
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 12105 | 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 |
| 12105 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 12105 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 12105
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 100 |
observation
- @ref: 67770
- observation: quinones: MK-9(III,VIII-H4), MK-9(H6)
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 12105 | sandy soil | Chokoria | Bangladesh | BGD | Asia |
| 67770 | Sandy soil at a forest-side waterfall | Chokoria, Cox's Bazar | Bangladesh | BGD | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Sandy |
| #Environmental | #Terrestrial | #Soil |
Safety information
risk assessment
- @ref: 12105
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 12105
- description: Sphaerisporangium rubeum gene for 16S rRNA, partial sequence, strain: 3D-72(35)
- accession: AB208718
- length: 1502
- database: ena
- NCBI tax ID: 321317
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sphaerisporangium rubeum DSM 44936 | GCA_014207705 | contig | ncbi | 321317 |
| 66792 | Sphaerisporangium rubeum strain DSM 44936 | 321317.3 | wgs | patric | 321317 |
| 66792 | Sphaerisporangium rubeum DSM 44936 | 2863055337 | draft | img | 321317 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 12105 | 71 | |
| 67770 | 71 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| gram-positive | yes | 89.266 | no |
| anaerobic | no | 98.73 | yes |
| halophile | no | 94.407 | no |
| spore-forming | yes | 89.013 | no |
| glucose-util | yes | 84.02 | no |
| aerobic | yes | 91.727 | yes |
| thermophile | no | 96.587 | yes |
| motile | no | 93.967 | no |
| flagellated | no | 98.497 | no |
| glucose-ferment | no | 93.586 | no |
External links
@ref: 12105
culture collection no.: DSM 44936, JCM 13067, BCC 36479, CGMCC 4.5529, TBRC 573
straininfo link
- @ref: 85646
- straininfo: 297456
literature
- topic: Phylogeny
- Pubmed-ID: 26303767
- title: Sphaerisporangium aureirubrum sp. nov., an actinomycete isolated from soil.
- authors: Guo L, Zhao J, Liu C, Bai L, Sun P, Han C, Li J, Guo X, Xiang W, Wang X
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.000554
- year: 2015
- mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Transcriptome
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 12105 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44936) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-44936 | |
| 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 | |
| 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 | |
| 85646 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID297456.1 | StrainInfo: A central database for resolving microbial strain identifiers |