Strain identifier
BacDive ID: 24803
Type strain: 
Species: Motilibacter rhizosphaerae
Strain Designation: RS-16
Strain history: KACC 16209 <-- S. D. Lee; Jeju Natl. Univ., South Korea; RS-16.
NCBI tax ID(s): 598652 (species)
version 9.1 (current version)
General
@ref: 21229
BacDive-ID: 24803
DSM-Number: 45622
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-positive, rod-shaped
description: Motilibacter rhizosphaerae RS-16 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from soil of the rhizosphere of Peucedanum japonicum Thunb..
NCBI tax id
- NCBI tax id: 598652
- Matching level: species
strain history
| @ref | history |
|---|---|
| 21229 | <- S. D. Lee, Jeju National Univ., Rep. of Korea; RS-16 |
| 67770 | KACC 16209 <-- S. D. Lee; Jeju Natl. Univ., South Korea; RS-16. |
doi: 10.13145/bacdive24803.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Motilibacterales
- family: Motilibacteraceae
- genus: Motilibacter
- species: Motilibacter rhizosphaerae
- full scientific name: Motilibacter rhizosphaerae Lee 2013
@ref: 21229
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Motilibacteraceae
genus: Motilibacter
species: Motilibacter rhizosphaerae
full scientific name: Motilibacter rhizosphaerae Lee 2013
strain designation: RS-16
type strain: yes
Morphology
cell morphology
- @ref: 31110
- gram stain: positive
- cell length: 1.45 µm
- cell width: 0.79 µm
- cell shape: rod-shaped
- motility: no
pigmentation
- @ref: 31110
- production: yes
multimedia
- @ref: 21229
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45622.jpg
- caption: Medium 553 28°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 21229 | ISP2 MEDIUM (DSMZ Medium 987) | yes | https://mediadive.dsmz.de/medium/987 | Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water |
| 21229 | GPHF-MEDIUM (DSMZ Medium 553) | yes | https://mediadive.dsmz.de/medium/553 | Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 21229 | positive | growth | 28 |
| 31110 | positive | growth | 20-37 |
| 31110 | positive | optimum | 37 |
| 67770 | positive | growth | 28 |
culture pH
- @ref: 31110
- ability: positive
- type: growth
- pH: 6.0-7.0
Physiology and metabolism
oxygen tolerance
- @ref: 31110
- oxygen tolerance: aerobe
spore formation
- @ref: 31110
- spore formation: no
observation
| @ref | observation |
|---|---|
| 31110 | aggregates in clumps |
| 67770 | quinones: MK-9(H4) |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 31110 | 15963 | ribitol | + | carbon source |
| 31110 | 23652 | dextrin | + | carbon source |
| 31110 | 17306 | maltose | + | carbon source |
| 31110 | 28053 | melibiose | + | carbon source |
| 31110 | 16634 | raffinose | + | carbon source |
| 31110 | 17151 | xylitol | + | carbon source |
| 31110 | 4853 | esculin | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 31110 | acid phosphatase | + | 3.1.3.2 |
| 31110 | alkaline phosphatase | + | 3.1.3.1 |
| 31110 | catalase | + | 1.11.1.6 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 21229 | soil of the rhizosphere of Peucedanum japonicum Thunb. | Peucedanum japonicum | Jeju, Mara Island | Republic of Korea | KOR | Asia |
| 67770 | Rhizosphere soil of a wild plant (Peucedanum japonicum Thunb.) on Mara Island in Jeju | Peucedanum japonicum | Republic of Korea | KOR | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Rhizosphere |
taxonmaps
- @ref: 69479
- File name: preview.99_58446.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_25869;97_32451;98_41614;99_58446&stattab=map
- Last taxonomy: Motilibacter rhizosphaerae subclade
- 16S sequence: FM998018
- Sequence Identity:
- Total samples: 153
- soil counts: 131
- aquatic counts: 9
- animal counts: 9
- plant counts: 4
Safety information
risk assessment
- @ref: 21229
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21229
- description: Motilibacter rhizosphaerae strain RS-16 16S ribosomal RNA gene, partial sequence
- accession: FM998018
- length: 1423
- database: nuccore
- NCBI tax ID: 598652
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Motilibacter rhizosphaerae strain DSM 45622 | 598652.3 | wgs | patric | 598652 |
| 66792 | Motilibacter rhizosphaerae DSM 45622 | 2799112218 | draft | img | 598652 |
| 67770 | Motilibacter rhizosphaerae DSM 45622 | GCA_004216915 | scaffold | ncbi | 598652 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 21229 | 73.1 | |
| 67770 | 73.1 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 82 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | yes | 88.791 | yes |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 93.979 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 52.138 | yes |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 77.729 | yes |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 97.318 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 61.75 | no |
External links
@ref: 21229
culture collection no.: DSM 45622, KACC 16209, JCM 32087
straininfo link
- @ref: 88625
- straininfo: 400016
literature
- topic: Phylogeny
- Pubmed-ID: 23667142
- title: Proposal of Motilibacteraceae fam. nov., with the description of Motilibacter rhizosphaerae sp. nov.
- authors: Lee SD
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.052357-0
- year: 2013
- mesh: Actinomycetales/*classification/genetics/isolation & purification, Apiaceae/microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysis
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 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 | ||||
| 21229 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45622 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45622) | ||||
| 31110 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27439 | 28776041 | ||
| 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 | ||||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
| 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 | ||||
| 88625 | 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-ID400016.1 |