Strain identifier
BacDive ID: 13870
Type strain:
Species: Rhodobium orientis
Strain history: A. Hiraishi MB312.
NCBI tax ID(s): 34017 (species)
General
@ref: 4281
BacDive-ID: 13870
DSM-Number: 11290
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative
description: Rhodobium orientis DSM 11290 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from coastal seawater.
NCBI tax id
- NCBI tax id: 34017
- Matching level: species
strain history
@ref | history |
---|---|
4281 | <- JCM <- A. Hiraishi, MB 312 |
67770 | A. Hiraishi MB312. |
doi: 10.13145/bacdive13870.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Rhodobiaceae
- genus: Rhodobium
- species: Rhodobium orientis
- full scientific name: Rhodobium orientis Hiraishi et al. 1995
@ref: 4281
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Rhodobiaceae
genus: Rhodobium
species: Rhodobium orientis
full scientific name: Rhodobium orientis Hiraishi et al. 1995 emend. Urdiain et al. 2008
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.998
Culture and growth conditions
culture medium
- @ref: 4281
- name: RHODOBIUM MEDIUM (DSMZ Medium 745)
- growth: yes
- link: https://mediadive.dsmz.de/medium/745
- composition: Name: RHODOBIUM MEDIUM (DSMZ Medium 745) Composition: NaCl 50.2 g/l Na-DL-malate 3.6 g/l Yeast extract 1.0 g/l KH2PO4 1.0 g/l (NH4)2SO4 1.0 g/l Na2S2O3 x 5 H2O 0.5 g/l MgCl2 x 6 H2O 0.2 g/l CaCl2 x 2 H2O 0.05 g/l Na2-EDTA 0.0052 g/l FeCl2 x 4 H2O 0.0015 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l H3BO3 6.2e-05 g/l Na2MoSO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l CuCl2 x 2 H2O 1.7e-05 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
4281 | positive | growth | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 4281
- oxygen tolerance: anaerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.996 |
observation
- @ref: 67770
- observation: quinones: Q-10, MK-10
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
4281 | coastal seawater | Makurazaki | Japan | JPN | Asia |
67770 | Coastal seawater | Makurazaki | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Terrestrial | #Coast |
taxonmaps
- @ref: 69479
- File name: preview.99_60542.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_26621;97_33425;98_42966;99_60542&stattab=map
- Last taxonomy: Rhodobium
- 16S sequence: D30792
- Sequence Identity:
- Total samples: 1047
- soil counts: 181
- aquatic counts: 736
- animal counts: 81
- plant counts: 49
Safety information
risk assessment
- @ref: 4281
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Rhodobium orientis strain DSM 11290 16S-23S ribosomal RNA intergenic spacer, partial sequence | EU786783 | 700 | ena | 34017 |
4281 | Rhodobium orientis 16S rRNA gene, complete sequence | D30792 | 1408 | ena | 34017 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Rhodobium orientis DSM 11290 | GCA_014197785 | contig | ncbi | 34017 |
66792 | Rhodobium orientis DSM 11290 | GCA_016653375 | scaffold | ncbi | 34017 |
66792 | Rhodobium orientis DSM 11290 | GCA_003258835 | scaffold | ncbi | 34017 |
66792 | Rhodobium orientis strain DSM 11290 | 34017.7 | wgs | patric | 34017 |
66792 | Rhodobium orientis strain DSM 11290 | 34017.6 | wgs | patric | 34017 |
66792 | Rhodobium orientis strain DSM 11290 | 34017.4 | wgs | patric | 34017 |
66792 | Rhodobium orientis DSM 11290 | 2887616557 | draft | img | 34017 |
66792 | Rhodobium orientis DSM 11290 | 2838101865 | draft | img | 34017 |
GC content
- @ref: 4281
- GC-content: 65.3
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 62.704 | no |
gram-positive | no | 98.517 | no |
anaerobic | no | 65.116 | yes |
aerobic | no | 65.403 | no |
halophile | no | 65.198 | no |
spore-forming | no | 95.772 | no |
thermophile | no | 88.537 | yes |
glucose-util | yes | 90.204 | no |
motile | yes | 83.166 | no |
glucose-ferment | no | 90.332 | no |
External links
@ref: 4281
culture collection no.: DSM 11290, JCM 9337, ATCC 51972, NCIMB 13423
straininfo link
- @ref: 83046
- straininfo: 43269
literature
- topic: Phylogeny
- Pubmed-ID: 17473235
- title: Rhodobium gokarnense sp. nov., a novel phototrophic alphaproteobacterium from a saltern.
- authors: Srinivas TNR, Kumar PA, Sasikala C, Ramana CV, Imhoff JF
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.64843-0
- year: 2007
- mesh: Alphaproteobacteria/chemistry/*classification/*isolation & purification/physiology, Bacteriochlorophyll A/analysis, Carbon/metabolism, Carotenoids/analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fermentation, Genes, rRNA/genetics, India, Molecular Sequence Data, Nucleic Acid Hybridization, Organelles/ultrastructure, Peptones/metabolism, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, *Water Microbiology
- topic2: Metabolism
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4281 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11290) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-11290 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
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 | |
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. | 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 | |||
83046 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID43269.1 | StrainInfo: A central database for resolving microbial strain identifiers |