Strain identifier
BacDive ID: 13847
Type strain: 
Species: Shimia litoralis
Strain Designation: CL-ES2
Strain history: <- B. C. Cho, Seoul Natl. Univ., Republic of Korea; CL-ES2
NCBI tax ID(s): 1122945 (strain), 420403 (species)
version 8.1 (current version)
General
@ref: 7486
BacDive-ID: 13847
DSM-Number: 18290
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, coccus-shaped
description: Shimia litoralis CL-ES2 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from coastal water .
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 420403 | species |
| 1122945 | strain |
strain history
- @ref: 7486
- history: <- B. C. Cho, Seoul Natl. Univ., Republic of Korea; CL-ES2
doi: 10.13145/bacdive13847.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Shimia
- species: Shimia litoralis
- full scientific name: Shimia litoralis (Kim et al. 2008) Zhang et al. 2023
synonyms
- @ref: 20215
- synonym: Pelagicola litoralis
@ref: 7486
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Pelagicola
species: Pelagicola litoralis
full scientific name: Pelagicola litoralis Kim et al. 2008
strain designation: CL-ES2
type strain: yes
Morphology
cell morphology
- @ref: 32633
- gram stain: negative
- cell length: 1.2-1.8 µm
- cell width: 0.5-0.9 µm
- cell shape: coccus-shaped
- motility: no
pigmentation
- @ref: 32633
- production: yes
Culture and growth conditions
culture medium
- @ref: 7486
- 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 |
|---|---|---|---|---|
| 7486 | positive | growth | 28 | mesophilic |
| 32633 | positive | growth | 20-30 | |
| 32633 | positive | optimum | 25 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 32633 | positive | growth | 06-08 |
| 32633 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 32633
- oxygen tolerance: aerobe
spore formation
- @ref: 32633
- spore formation: no
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 32633 | NaCl | positive | growth | 02-06 % |
| 32633 | NaCl | positive | optimum | 03-04 % |
observation
- @ref: 32633
- observation: aggregates in chains
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32633 | 30089 | acetate | + | carbon source |
| 32633 | 17234 | glucose | + | carbon source |
| 32633 | 26271 | proline | + | carbon source |
| 32633 | 17822 | serine | + | carbon source |
| 32633 | 53426 | tween 80 | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 32633 | catalase | + | 1.11.1.6 |
| 32633 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 7486
- sample type: coastal water (East Sea)
- geographic location: east coast of Korea
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
Safety information
risk assessment
- @ref: 7486
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7486
- description: Pelagicola litoralis strain CL-ES2 16S ribosomal RNA gene, partial sequence
- accession: EF192392
- length: 1382
- database: ena
- NCBI tax ID: 420403
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pelagicola litoralis CL-ES2 | GCA_005518135 | contig | ncbi | 420403 |
| 66792 | Pelagicola litoralis DSM 18290 | 2574179735 | draft | img | 1122945 |
| 66792 | Pelagicola litoralis CL-ES2 | 2890059200 | draft | img | 420403 |
GC content
| @ref | GC-content |
|---|---|
| 7486 | 47.0 |
| 32633 | 47 |
External links
@ref: 7486
culture collection no.: DSM 18290, KCCM 42274
straininfo link
- @ref: 83023
- straininfo: 405538
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 18768612 | Pelagicola litoralis gen. nov., sp. nov., isolated from coastal water in Korea. | Kim YG, Hwang CY, Cho BC | Int J Syst Evol Microbiol | 10.1099/ijs.0.65820-0 | 2008 | Aerobiosis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Hydrogen-Ion Concentration, Korea, Locomotion, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Salts/metabolism, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Temperature | Genetics |
| Phylogeny | 21890723 | Planktotalea frisia gen. nov., sp. nov., isolated from the southern North Sea. | Hahnke S, Tindall BJ, Schumann P, Sperling M, Brinkhoff T, Simon M | Int J Syst Evol Microbiol | 10.1099/ijs.0.033563-0 | 2011 | Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Culture Media/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Heterotrophic Processes, Hydrogen-Ion Concentration, Molecular Sequence Data, North Sea, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, Temperature | Genetics |
| Phylogeny | 23828179 | Roseovarius marisflavi sp. nov., isolated from an amphioxus breeding zone in the coastal region of the Yellow Sea, China. | Li Z, Zhao R, Ji S, Shi X, Zhang XH | Antonie Van Leeuwenhoek | 10.1007/s10482-013-9965-6 | 2013 | Aerobiosis, Animals, Bacterial Proteins/analysis, Base Composition, Catalase/analysis, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Hydroxybutyrates/analysis, Lancelets/*growth & development, Molecular Sequence Data, Oxidoreductases/analysis, Phospholipids/analysis, Phylogeny, Polyesters/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature | Genetics |
| Phylogeny | 31647402 | Pelagicola marinus sp. nov. isolated from deep-sea water. | Choi YS, Oh JS, Roh DH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003764 | 2019 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, 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 | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 7486 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18290) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18290 | ||||
| 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 | ||||
| 32633 | 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 | 28844 | 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 | ||
| 83023 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID405538.1 | StrainInfo: A central database for resolving microbial strain identifiers |