Strain identifier
BacDive ID: 13779
Type strain: 
Species: Rubellimicrobium roseum
Strain history: <- S.-K. Tang, YIM; YIM 48858 <- Y.-R. Cao
NCBI tax ID(s): 687525 (species)
version 8.1 (current version)
General
@ref: 17231
BacDive-ID: 13779
DSM-Number: 23580
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Rubellimicrobium roseum DSM 23580 is a mesophilic, Gram-negative bacterium that was isolated from forest soil.
NCBI tax id
- NCBI tax id: 687525
- Matching level: species
strain history
- @ref: 17231
- history: <- S.-K. Tang, YIM; YIM 48858 <- Y.-R. Cao
doi: 10.13145/bacdive13779.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Rubellimicrobium
- species: Rubellimicrobium roseum
- full scientific name: Rubellimicrobium roseum Cao et al. 2013
@ref: 17231
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Rubellimicrobium
species: Rubellimicrobium roseum
full scientific name: Rubellimicrobium roseum Cao et al. 2013
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.956
Culture and growth conditions
culture medium
- @ref: 17231
- 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: 17231
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 96 |
| 69480 | no | 99.975 |
Isolation, sampling and environmental information
isolation
- @ref: 17231
- sample type: forest soil
- geographic location: Yunnan province
- country: China
- origin.country: CHN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Forest |
| #Environmental | #Terrestrial | #Soil |
Safety information
risk assessment
- @ref: 17231
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17231
- description: Rubellimicrobium roseum strain YIM 48858 16S ribosomal RNA gene, partial sequence
- accession: GU109478
- length: 1466
- database: ena
- NCBI tax ID: 687525
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rubellimicrobium roseum YIM 48858 | GCA_006152145 | contig | ncbi | 687525 |
| 66792 | Rubellimicrobium roseum strain YIM 48858 | 687525.3 | wgs | patric | 687525 |
GC content
- @ref: 17231
- GC-content: 67.7
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 96 | no |
| gram-positive | no | 97.164 | no |
| anaerobic | no | 97.379 | no |
| halophile | no | 74.142 | no |
| spore-forming | no | 94.338 | no |
| glucose-util | yes | 88.536 | no |
| thermophile | no | 96.622 | yes |
| flagellated | no | 91.915 | no |
| motile | no | 70.632 | no |
| aerobic | yes | 91.761 | no |
| glucose-ferment | no | 88.686 | no |
External links
@ref: 17231
culture collection no.: DSM 23580, CCTCC AA 208029, KCTC 23202, YIM 48858
straininfo link
- @ref: 82958
- straininfo: 404077
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 20567903 | Rubellimicrobium roseum sp. nov., a Gram-negative bacterium isolated from the forest soil sample. | Cao YR, Jiang Y, Wang Q, Tang SK, He WX, Xue QH, Xu LH, Jiang CL | Antonie Van Leeuwenhoek | 10.1007/s10482-010-9452-2 | 2010 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/*analysis, DNA, Ribosomal/analysis, Genes, rRNA, Hot Temperature, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Soil, *Soil Microbiology | Stress |
| Phylogeny | 31346832 | Rubellimicrobium rubrum sp. nov., a novel bright reddish bacterium isolated from a lichen sample. | Jiang LQ, Zhang K, Li GD, Wang XY, Shi SB, Li QY, An DF, Lang L, Wang LS, Jiang CL, Jiang Y | Antonie Van Leeuwenhoek | 10.1007/s10482-019-01304-5 | 2019 | Aerobiosis, *Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Glycolipids/analysis, Hydrogen-Ion Concentration, Lichens/*microbiology, Locomotion, Phospholipids/analysis, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 17231 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23580) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23580 | |||
| 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) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 82958 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID404077.1 | StrainInfo: A central database for resolving microbial strain identifiers |