Strain identifier
BacDive ID: 13778
Type strain: 
Species: Rubellimicrobium aerolatum
Strain Designation: 5715S-9
Strain history: <- S.-W. Kwon, KACC; 5715S-9 <- H.-Y. Weon
NCBI tax ID(s): 1123066 (strain), 490979 (species)
version 8.1 (current version)
General
@ref: 8003
BacDive-ID: 13778
DSM-Number: 19297
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Rubellimicrobium aerolatum 5715S-9 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Air sample.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 1123066 | strain |
| 490979 | species |
strain history
- @ref: 8003
- history: <- S.-W. Kwon, KACC; 5715S-9 <- H.-Y. Weon
doi: 10.13145/bacdive13778.20230509.8.1
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 aerolatum
- full scientific name: Rubellimicrobium aerolatum Weon et al. 2009
@ref: 8003
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Rubellimicrobium
species: Rubellimicrobium aerolatum
full scientific name: Rubellimicrobium aerolatum Weon et al. 2009
strain designation: 5715S-9
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 32656 | negative | 2.6 µm | 0.8 µm | rod-shaped | no | |
| 69480 | negative | 99.996 |
Culture and growth conditions
culture medium
- @ref: 8003
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 8003 | positive | growth | 28 | mesophilic |
| 32656 | positive | growth | 05-35 | |
| 32656 | positive | optimum | 30 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 32656 | positive | growth | 06-07 |
| 32656 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 32656
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 32656 | no | |
| 69480 | no | 99.997 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 32656 | NaCl | positive | growth | 0-1 % |
| 32656 | NaCl | positive | optimum | 0.5 % |
observation
- @ref: 32656
- observation: aggregates in clumps
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 32656 | alkaline phosphatase | + | 3.1.3.1 |
| 32656 | catalase | + | 1.11.1.6 |
| 32656 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 8003
- sample type: Air sample
- geographic location: Suwon
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
isolation source categories
- Cat1: #Environmental
- Cat2: #Air
taxonmaps
- @ref: 69479
- File name: preview.99_14776.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_532;96_2715;97_9132;98_11194;99_14776&stattab=map
- Last taxonomy: Rubellimicrobium aerolatum subclade
- 16S sequence: EU338486
- Sequence Identity:
- Total samples: 256
- soil counts: 55
- aquatic counts: 56
- animal counts: 142
- plant counts: 3
Safety information
risk assessment
- @ref: 8003
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 8003
- description: Rubellimicrobium aerolatum strain 5715S-9 16S ribosomal RNA gene, partial sequence
- accession: EU338486
- length: 1354
- database: ena
- NCBI tax ID: 490979
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rubellimicrobium aerolatum DSM 19297 | GCA_017872975 | contig | ncbi | 490979 |
| 66792 | Rubellimicrobium aerolatum strain DSM 19297 | 490979.3 | wgs | patric | 490979 |
| 66792 | Rubellimicrobium aerolatum DSM 19297 | 2913276826 | draft | img | 490979 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 8003 | 69 | high performance liquid chromatography (HPLC) |
| 32656 | 69 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 55 | no |
| gram-positive | no | 98.125 | yes |
| anaerobic | no | 96.458 | no |
| halophile | no | 84.028 | no |
| spore-forming | no | 94.74 | yes |
| glucose-util | yes | 90.974 | no |
| aerobic | yes | 89.723 | yes |
| motile | no | 66.786 | yes |
| thermophile | no | 94.228 | yes |
| flagellated | no | 90.306 | yes |
| glucose-ferment | no | 88.045 | no |
External links
@ref: 8003
culture collection no.: DSM 19297, KACC 12504
straininfo link
- @ref: 82957
- straininfo: 397834
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19196786 | Rubellimicrobium aerolatum sp. nov., isolated from an air sample in Korea. | Weon HY, Son JA, Yoo SH, Hong SB, Jeon YA, Kwon SW, Koo BS | Int J Syst Evol Microbiol | 10.1099/ijs.0.65856-0 | 2009 | *Air Microbiology, Fatty Acids/analysis, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/chemistry/*classification/genetics/isolation & purification, Species Specificity | Genetics |
| 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 | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 8003 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19297) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19297 | |||
| 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 | |||
| 32656 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28867 | 28776041 | |
| 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) | |||
| 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 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) | |||
| 82957 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID397834.1 | StrainInfo: A central database for resolving microbial strain identifiers |