Strain identifier
BacDive ID: 130634
Type strain: 
Species: Ruegeria litorea
Strain Designation: R37
Strain history: <- CECT <- M. J. Pujalte, Univ. Valencia, Campus Burjasot, Spain; R37
NCBI tax ID(s): 1280831 (species)
version 8.1 (current version)
General
@ref: 22057
BacDive-ID: 130634
DSM-Number: 29947
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Ruegeria litorea R37 is a mesophilic, Gram-negative bacterium that was isolated from surface seawater.
NCBI tax id
- NCBI tax id: 1280831
- Matching level: species
strain history
- @ref: 22057
- history: <- CECT <- M. J. Pujalte, Univ. Valencia, Campus Burjasot, Spain; R37
doi: 10.13145/bacdive130634.20230509.8.1
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 litorea
- full scientific name: Ruegeria litorea (Lucena et al. 2014) Wirth and Whitman 2018
synonyms
@ref synonym 20215 Falsiruegeria litorea 20215 Tropicibacter litoreus
@ref: 22057
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Ruegeria
species: Ruegeria litorea
full scientific name: Ruegeria litorea (Lucena et al. 2014) Wirth and Whitman 2018
strain designation: R37
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.992
colony morphology
- @ref: 22057
- incubation period: 2-3 days
Culture and growth conditions
culture medium
- @ref: 22057
- 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: 22057
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.996 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 68369 | 25115 | malate | - | assimilation |
| 68369 | 17128 | adipate | - | assimilation |
| 68369 | 27689 | decanoate | - | assimilation |
| 68369 | 24265 | gluconate | - | assimilation |
| 68369 | 17306 | maltose | - | assimilation |
| 68369 | 59640 | N-acetylglucosamine | - | assimilation |
| 68369 | 16899 | D-mannitol | - | assimilation |
| 68369 | 16024 | D-mannose | - | assimilation |
| 68369 | 30849 | L-arabinose | - | assimilation |
| 68369 | 17634 | D-glucose | - | assimilation |
| 68369 | 5291 | gelatin | - | hydrolysis |
| 68369 | 4853 | esculin | - | hydrolysis |
| 68369 | 16199 | urea | - | hydrolysis |
| 68369 | 29016 | arginine | - | hydrolysis |
| 68369 | 17634 | D-glucose | - | fermentation |
| 68369 | 27897 | tryptophan | - | energy source |
| 68369 | 17632 | nitrate | + | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 22057 | catalase | + | 1.11.1.6 |
| 22057 | cytochrome-c oxidase | + | 1.9.3.1 |
| 68369 | gelatinase | - | |
| 68369 | beta-glucosidase | - | 3.2.1.21 |
| 68369 | urease | - | 3.5.1.5 |
| 68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
| @ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 22057 | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
- @ref: 22057
- sample type: surface seawater
- geographic location: Valencia, Malvarrosa Beach
- country: Spain
- origin.country: ESP
- continent: Europe
- latitude: 39.4747
- longitude: -0.3231
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Surface water |
taxonmaps
- @ref: 69479
- File name: preview.99_5221.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_2537;97_3099;98_3892;99_5221&stattab=map
- Last taxonomy: Ruegeria
- 16S sequence: HE860713
- Sequence Identity:
- Total samples: 816
- soil counts: 68
- aquatic counts: 723
- animal counts: 21
- plant counts: 4
Safety information
risk assessment
- @ref: 22057
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22057
- description: Tropicibacter litoreus R37 partial 16S rRNA gene, type strain R37T
- accession: HE860713
- length: 1399
- database: ena
- NCBI tax ID: 1200284
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Falsiruegeria litorea R37 CECT 7639 | GCA_900172225 | contig | ncbi | 1200284 |
| 66792 | Tropicibacter litoreus R37 strain CECT 7639 | 1200284.4 | wgs | patric | 1200284 |
| 66792 | Ruegeria litorea CECT 7639 | 2834189540 | draft | img | 1200284 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 51.155 | no |
| gram-positive | no | 98.315 | no |
| anaerobic | no | 99.299 | no |
| aerobic | yes | 96.631 | no |
| halophile | yes | 80.986 | no |
| spore-forming | no | 96.105 | no |
| thermophile | no | 96.762 | yes |
| glucose-util | no | 56.831 | yes |
| flagellated | no | 77.454 | no |
| glucose-ferment | no | 91.342 | yes |
External links
@ref: 22057
culture collection no.: DSM 29947, CECT 7639, KCTC 23353
straininfo link
- @ref: 89146
- straininfo: 392148
literature
- topic: Phylogeny
- Pubmed-ID: 23706913
- title: Description of Tropicibacter mediterraneus sp. nov. and Tropicibacter litoreus sp. nov.
- authors: Lucena T, Ruvira MA, Macian MC, Pujalte MJ, Arahal DR
- journal: Syst Appl Microbiol
- DOI: 10.1016/j.syapm.2013.04.001
- year: 2013
- mesh: Animals, Bacterial Proteins/analysis, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Molecular Sequence Data, Ostreidae/microbiology, Phylogeny, Proteome/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/chemistry/*classification/genetics/*isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Spain, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 22057 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29947 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29947) | |
| 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 | |
| 68369 | Automatically annotated from API 20NE | |||
| 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 | |
| 89146 | 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-ID392148.1 |