Strain identifier
BacDive ID: 130736
Type strain: 
Species: Sphaerisporangium rufum
Strain Designation: R10-82
Strain history: <- C Suriyachadkun, BIOTEC Culture Collection (BCC); BCC 51287 <- R. Mingma
NCBI tax ID(s): 1381558 (species)
version 8.1 (current version)
General
@ref: 21832
BacDive-ID: 130736
DSM-Number: 46862
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic
description: Sphaerisporangium rufum R10-82 is a spore-forming, mesophilic bacterium that was isolated from rice plant root.
NCBI tax id
- NCBI tax id: 1381558
- Matching level: species
strain history
- @ref: 21832
- history: <- C Suriyachadkun, BIOTEC Culture Collection (BCC); BCC 51287 <- R. Mingma
doi: 10.13145/bacdive130736.20230509.8.1
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 rufum
- full scientific name: Sphaerisporangium rufum Mingma et al. 2014
@ref: 21832
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptosporangiaceae
genus: Sphaerisporangium
species: Sphaerisporangium rufum
full scientific name: Sphaerisporangium rufum Mingma et al. 2014
strain designation: R10-82
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | no | 95.299 | |
| 69480 | 100 | positive |
multimedia
- @ref: 21832
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_46862.jpg
- caption: Medium 65 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 21832 | ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf | |
| 21832 | 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 |
culture temp
- @ref: 21832
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 100 |
Isolation, sampling and environmental information
isolation
- @ref: 21832
- sample type: rice plant root
- geographic location: Suphan Buri province
- country: Thailand
- origin.country: THA
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Root (Rhizome) |
taxonmaps
- @ref: 69479
- File name: preview.99_16336.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_239;96_8333;97_10032;98_12328;99_16336&stattab=map
- Last taxonomy: Sphaerisporangium rufum subclade
- 16S sequence: AB842299
- Sequence Identity:
- Total samples: 27
- soil counts: 18
- aquatic counts: 4
- animal counts: 4
- plant counts: 1
Safety information
risk assessment
- @ref: 21832
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21832
- description: Sphaerisporangium rufum gene for 16S ribosomal RNA, partial sequence
- accession: AB842299
- length: 1484
- database: ena
- NCBI tax ID: 1381558
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sphaerisporangium rufum NBRC 109079 | GCA_016863395 | contig | ncbi | 1381558 |
| 66792 | Sphaerisporangium rufum strain NBRC 109079 | 1381558.3 | wgs | patric | 1381558 |
GC content
- @ref: 21832
- GC-content: 74
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | no | 92.315 | no |
| gram-positive | yes | 90.372 | no |
| anaerobic | no | 99.023 | no |
| halophile | no | 90.625 | no |
| spore-forming | yes | 94.368 | no |
| thermophile | no | 97.554 | yes |
| glucose-util | yes | 85.839 | no |
| aerobic | yes | 91.2 | no |
| flagellated | no | 98.163 | no |
| glucose-ferment | no | 91.833 | no |
External links
@ref: 21832
culture collection no.: DSM 46862, BCC 51287, NBRC 109079
straininfo link
- @ref: 89236
- straininfo: 397788
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24363300 | Sphaerisporangium rufum sp. nov., an endophytic actinomycete from roots of Oryza sativa L. | Mingma R, Duangmal K, Trakulnaleamsai S, Thamchaipenet A, Matsumoto A, Takahashi Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.057885-0 | 2013 | Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Oryza/*microbiology, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/chemistry | Genetics |
| Phylogeny | 36253621 | Sphaerisporangium fuscum sp. nov., Isolated from Sediment of Anmucuo Lake in Tibet Autonomous Region of China. | Guo Y, Li J, Li L, Liu C | Curr Microbiol | 10.1007/s00284-022-03067-1 | 2022 | *Actinomycetales, Cardiolipins, DNA, Bacterial/chemistry/genetics, Diaminopimelic Acid/analysis/chemistry, Fatty Acids/chemistry, Glucose, Lakes/analysis, Nucleotides, Peptidoglycan/analysis, *Phosphatidylethanolamines, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Ribose, Sequence Analysis, DNA, Soil Microbiology, Tibet, Vitamin K 2/chemistry | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |
| 21832 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-46862 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 46862) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
| 89236 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID397788.1 |