Strain identifier
BacDive ID: 22986
Type strain: 
Species: Rudaeicoccus suwonensis
Strain Designation: HOR6-4
Strain history: <- S.-W. Kwon, KACC; HOR6-4
NCBI tax ID(s): 657409 (species)
version 8.1 (current version)
General
@ref: 19293
BacDive-ID: 22986
DSM-Number: 19560
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, coccus-shaped
description: Rudaeicoccus suwonensis HOR6-4 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from epidermal tissue of a surface-sterilized root of a Phalaenopsis orchid.
NCBI tax id
- NCBI tax id: 657409
- Matching level: species
strain history
- @ref: 19293
- history: <- S.-W. Kwon, KACC; HOR6-4
doi: 10.13145/bacdive22986.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Dermacoccaceae
- genus: Rudaeicoccus
- species: Rudaeicoccus suwonensis
- full scientific name: Rudaeicoccus suwonensis Kim et al. 2013
@ref: 19293
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Dermacoccaceae
genus: Rudaeicoccus
species: Rudaeicoccus suwonensis
full scientific name: Rudaeicoccus suwonensis Kim et al. 2013
strain designation: HOR6-4
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 30739 | positive | 0.7 µm | 0.7 µm | coccus-shaped | no | |
| 69480 | no | 97.88 | ||||
| 69480 | positive | 100 |
pigmentation
- @ref: 30739
- production: yes
Culture and growth conditions
culture medium
- @ref: 19293
- 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 |
|---|---|---|---|---|
| 19293 | positive | growth | 28 | mesophilic |
| 30739 | positive | growth | 10-37 | |
| 30739 | positive | optimum | 28 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 30739 | positive | growth | 04-09 | alkaliphile |
| 30739 | positive | optimum | 6.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 30739
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 30739 | no | |
| 69481 | no | 99 |
| 69480 | no | 99.991 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 30739 | NaCl | positive | growth | 0-5 % |
| 30739 | NaCl | positive | optimum | 0.5 % |
murein
- @ref: 19293
- murein short key: A11.57
- type: A4alpha L-Lys-L-Thr-D-Glu
observation
- @ref: 30739
- observation: aggregates in clumps
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30739 | 37054 | 3-hydroxybutyrate | + | carbon source |
| 30739 | 30089 | acetate | + | carbon source |
| 30739 | 16449 | alanine | + | carbon source |
| 30739 | 17234 | glucose | + | carbon source |
| 30739 | 27570 | histidine | + | carbon source |
| 30739 | 17306 | maltose | + | carbon source |
| 30739 | 37684 | mannose | + | carbon source |
| 30739 | 28053 | melibiose | + | carbon source |
| 30739 | 506227 | N-acetylglucosamine | + | carbon source |
| 30739 | 26271 | proline | + | carbon source |
| 30739 | 17272 | propionate | + | carbon source |
| 30739 | 33942 | ribose | + | carbon source |
| 30739 | 17814 | salicin | + | carbon source |
| 30739 | 17822 | serine | + | carbon source |
| 30739 | 17992 | sucrose | + | carbon source |
| 30739 | 31011 | valerate | + | carbon source |
| 30739 | 4853 | esculin | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30739 | acid phosphatase | + | 3.1.3.2 |
| 30739 | alpha-galactosidase | + | 3.2.1.22 |
| 30739 | gelatinase | + | |
| 30739 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
- @ref: 19293
- sample type: epidermal tissue of a surface-sterilized root of a Phalaenopsis orchid
- host species: Phalaenopsis
- geographic location: Suwon region
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Root (Rhizome) |
| #Host Body-Site | #Plant | #Sterilized plant part |
taxonmaps
- @ref: 69479
- File name: preview.99_45914.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_20999;97_26157;98_33244;99_45914&stattab=map
- Last taxonomy: Flexivirga
- 16S sequence: GQ241687
- Sequence Identity:
- Total samples: 47
- soil counts: 5
- aquatic counts: 18
- animal counts: 19
- plant counts: 5
Safety information
risk assessment
- @ref: 19293
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19293
- description: Rudaeicoccus suwonensis strain HOR6-4 16S ribosomal RNA gene, partial sequence
- accession: GQ241687
- length: 1394
- database: ena
- NCBI tax ID: 657409
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rudaeicoccus suwonensis DSM 19560 | GCA_007829035 | contig | ncbi | 657409 |
| 66792 | Rudaeicoccus suwonensis strain DSM 19560 | 657409.3 | wgs | patric | 657409 |
| 66792 | Rudaeicoccus suwonensis DSM 19560 | 2818991236 | draft | img | 657409 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 19293 | 65 | high performance liquid chromatography (HPLC) |
| 30739 | 65 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 99 | no |
| gram-positive | yes | 90.641 | yes |
| anaerobic | no | 98.844 | yes |
| halophile | no | 94.49 | no |
| spore-forming | no | 81.884 | no |
| glucose-util | yes | 89.71 | no |
| thermophile | no | 97.769 | yes |
| flagellated | no | 98.017 | no |
| aerobic | yes | 92.26 | no |
| glucose-ferment | no | 89.36 | no |
| motile | no | 95.452 | no |
External links
@ref: 19293
culture collection no.: DSM 19560, KACC 12637
straininfo link
- @ref: 87232
- straininfo: 405630
literature
- topic: Phylogeny
- Pubmed-ID: 22798654
- title: Rudaeicoccus suwonensis gen. nov., sp. nov., an actinobacterium isolated from the epidermal tissue of a root of a Phalaenopsis orchid.
- authors: Kim SJ, Jang YH, Ahn JH, Weon HY, Schumann P, Chun SC, Kwon SW, Kim WG
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.043455-0
- year: 2012
- mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Orchidaceae/*microbiology, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, Plant Epidermis/microbiology, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 19293 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19560) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19560 | ||||
| 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 | ||||
| 30739 | 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 | 27070 | 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) | ||||
| 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 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 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) | ||||
| 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 | ||||
| 87232 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID405630.1 | StrainInfo: A central database for resolving microbial strain identifiers |