Strain identifier
BacDive ID: 24505
Type strain: 
Species: Ruegeria intermedia
Strain Designation: CC-GIMAT-2
Variant: Isotype of BacDive ID 132916 & 130627
Strain history: <- P. Kämpfer, Univ. Giessen, Germany; CC-GIMAT-2 <- A. B. Arun
NCBI tax ID(s): 996115 (species)
version 8.1 (current version)
General
@ref: 20793
BacDive-ID: 24505
DSM-Number: 23285
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Ruegeria intermedia CC-GIMAT-2 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from coastal hot spring of a volcanic island.
NCBI tax id
- NCBI tax id: 996115
- Matching level: species
strain history
- @ref: 20793
- history: <- P. Kämpfer, Univ. Giessen, Germany; CC-GIMAT-2 <- A. B. Arun
doi: 10.13145/bacdive24505.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Ruegeria
- species: Ruegeria intermedia
- full scientific name: Ruegeria intermedia Kämpfer et al. 2013
@ref: 20793
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Ruegeria
species: Ruegeria intermedia
full scientific name: Ruegeria intermedia Kämpfer et al. 2013
strain designation: CC-GIMAT-2
variant: Isotype of BacDive ID 132916 & 130627
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 30935 | negative | 3.5 µm | 1.1 µm | rod-shaped | no | |
| 69480 | negative | 99.997 |
pigmentation
- @ref: 30935
- production: yes
Culture and growth conditions
culture medium
- @ref: 20793
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 20793 | positive | growth | 28 | mesophilic |
| 30935 | positive | growth | 15-55 | |
| 30935 | positive | optimum | 41 | thermophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 30935 | positive | growth | 5.0-10.0 | alkaliphile |
| 30935 | positive | optimum | 8 |
Physiology and metabolism
oxygen tolerance
- @ref: 30935
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 30935 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.997 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 30935 | NaCl | positive | growth | 01-04 % |
| 30935 | NaCl | positive | optimum | 1.5 % |
observation
- @ref: 30935
- observation: aggregates in clumps
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30935 | 28260 | galactose | + | carbon source |
| 30935 | 17234 | glucose | + | carbon source |
| 30935 | 4853 | esculin | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30935 | catalase | + | 1.11.1.6 |
| 30935 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 20793
- sample type: coastal hot spring of a volcanic island
- geographic location: Green Island (Lutao) of the Pacific Ocean, off the east coast of Taiwan (22°39' N 121° 29' E)
- country: Taiwan
- origin.country: TWN
- continent: Asia
- latitude: 22.65
- longitude: 121.483
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Thermal spring |
| #Environmental | #Terrestrial | #Volcanic |
| #Condition | #Thermophilic (>45°C) |
Safety information
risk assessment
- @ref: 20793
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20793
- description: Ruegeria intermedia partial 16S rRNA gene, type strain CC-GIMAT-2T
- accession: FR832879
- length: 1344
- database: ena
- NCBI tax ID: 996115
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Ruegeria intermedia DSM 29341 | GCA_900129345 | scaffold | ncbi | 996115 |
| 66792 | Ruegeria intermedia strain DSM 29341 | 996115.4 | wgs | patric | 996115 |
| 66792 | Ruegeria intermedia DSM 29341 | 2695420938 | draft | img | 996115 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 62.627 | yes |
| flagellated | no | 80.584 | yes |
| gram-positive | no | 98.285 | yes |
| anaerobic | no | 97.674 | yes |
| aerobic | yes | 86.938 | yes |
| halophile | yes | 65.03 | yes |
| spore-forming | no | 96.612 | yes |
| thermophile | no | 79.317 | no |
| glucose-util | yes | 62.647 | no |
| glucose-ferment | no | 91.13 | no |
External links
@ref: 20793
culture collection no.: DSM 23285, CCM 7758, CCUG 59209, DSM 104504, DSM 29341, LMG 25539
straininfo link
- @ref: 88363
- straininfo: 368608
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 23243093 | Ruegeria intermedia sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring. | Kampfer P, Arun AB, Rekha PD, Busse HJ, Young CC, Glaeser SP | Int J Syst Evol Microbiol | 10.1099/ijs.0.047910-0 | 2012 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Hot Springs/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Spermidine/analysis, Taiwan, Ubiquinone/analogs & derivatives/analysis | Genetics |
| Phylogeny | 29022541 | Ruegeria profundi sp. nov. and Ruegeria marisrubri sp. nov., isolated from the brine-seawater interface at Erba Deep in the Red Sea. | Zhang G, Haroon MF, Zhang R, Dong X, Wang D, Liu Y, Xun W, Dong X, Stingl U | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002344 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Indian Ocean, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, *Salts, Saudi Arabia, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
| Phylogeny | 32195650 | Ruegeria sediminis sp. nov., isolated from tidal flat sediment. | Baek J, Kim JH, Sukhoom A, Kim W | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004128 | 2020 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/isolation & purification, Seawater/microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 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 | |||
| 20793 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23285 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23285) | |||
| 30935 | 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 | 27265 | 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 | |||
| 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 | |||
| 88363 | 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-ID368608.1 |