Strain identifier
BacDive ID: 8210
Type strain: 
Species: Paraperlucidibaca baekdonensis
Strain Designation: RL-2
Strain history: <- JH Yoon, KRIBB
NCBI tax ID(s): 748120 (species)
version 8.1 (current version)
General
@ref: 18150
BacDive-ID: 8210
DSM-Number: 26022
keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-negative
description: Paraperlucidibaca baekdonensis RL-2 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from seawater.
NCBI tax id
- NCBI tax id: 748120
- Matching level: species
strain history
| @ref | history |
|---|---|
| 18150 | <- KCTC <- J.-H. Yoon, Korea Res. Inst. Biosci. & Biotechnol. (KRIBB), Taejon, South Korea; RL-2 |
| 67771 | <- JH Yoon, KRIBB |
doi: 10.13145/bacdive8210.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Pseudomonadales
- family: Moraxellaceae
- genus: Paraperlucidibaca
- species: Paraperlucidibaca baekdonensis
- full scientific name: Paraperlucidibaca baekdonensis Oh et al. 2011
@ref: 18150
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Moraxellaceae
genus: Paraperlucidibaca
species: Paraperlucidibaca baekdonensis
full scientific name: Paraperlucidibaca baekdonensis Oh et al. 2011
strain designation: RL-2
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 67771 | negative | |
| 69480 | negative | 99.998 |
colony morphology
| @ref | incubation period |
|---|---|
| 18150 | 3-7 days |
| 61900 | >3 days |
Culture and growth conditions
culture medium
- @ref: 18150
- name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830c
- composition: Name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 18150 | positive | growth | 20 | psychrophilic |
| 61900 | positive | growth | 20-30 | |
| 67771 | positive | growth | 20-25 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 61900 | aerobe |
| 67771 | aerobe |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 100 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|---|
| 18150 | seawater | East Sea, Baekdo Harbor | Republic of Korea | KOR | Asia | |
| 61900 | Seawater | East Sea,Baekdo harbor | Republic of Korea | KOR | Asia | 2008 |
| 67771 | From seawater | East Sea | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_62634.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_669;96_3622;97_34402;98_44352;99_62634&stattab=map
- Last taxonomy: Paraperlucidibaca baekdonensis
- 16S sequence: GU731671
- Sequence Identity:
- Total samples: 328
- soil counts: 9
- aquatic counts: 297
- animal counts: 22
Safety information
risk assessment
- @ref: 18150
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 18150
- description: Paraperlucidibaca baekdonensis strain RL-2 16S ribosomal RNA gene, partial sequence
- accession: GU731671
- length: 1460
- database: ena
- NCBI tax ID: 748120
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Paraperlucidibaca baekdonensis DSM 26022 | GCA_003387535 | scaffold | ncbi | 748120 |
| 66792 | Paraperlucidibaca baekdonensis strain DSM 26022 | 748120.3 | wgs | patric | 748120 |
| 66792 | Paraperlucidibaca baekdonensis DSM 26022 | 2770939643 | draft | img | 748120 |
GC content
- @ref: 18150
- GC-content: 61.3
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 85.476 | no |
| flagellated | yes | 53.525 | no |
| gram-positive | no | 99.063 | yes |
| anaerobic | no | 98.738 | yes |
| aerobic | yes | 87.595 | yes |
| halophile | no | 80.96 | no |
| spore-forming | no | 96.497 | no |
| glucose-util | no | 86.649 | no |
| thermophile | no | 98.03 | yes |
| glucose-ferment | no | 93.045 | no |
External links
@ref: 18150
culture collection no.: DSM 26022, CCUG 59307, KCTC 23145
straininfo link
- @ref: 77613
- straininfo: 407422
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 20601489 | Paraperlucidibaca baekdonensis gen. nov., sp. nov., isolated from seawater. | Oh KH, Lee SY, Lee MH, Oh TK, Yoon JH | Int J Syst Evol Microbiol | 10.1099/ijs.0.023994-0 | 2010 | Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Moraxellaceae/*classification/genetics/*isolation & purification/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Ubiquinone/analysis | Genetics |
| Phylogeny | 23749278 | Paraperlucidibaca wandonensis sp. nov., isolated from seawater, and emended description of the genus Paraperlucidibaca Oh et al. 2011. | Yoon JH, Park S, Jung YT, Lee JS, Lee KC | Int J Syst Evol Microbiol | 10.1099/ijs.0.048645-0 | 2013 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Moraxellaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry, Water Microbiology | Genetics |
| Phylogeny | 30783797 | Amnimonas aquatica gen. nov., sp. nov., Isolated from a Freshwater River. | Lee Y, Park HY, Jeon CO | Curr Microbiol | 10.1007/s00284-019-01652-5 | 2019 | Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial/genetics, Moraxellaceae/chemistry/*classification/genetics/*physiology, Nucleic Acid Hybridization, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rivers/*microbiology, Sequence Analysis, DNA, Species Specificity, Ubiquinone/chemistry, *Water Microbiology | Phenotype |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 18150 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26022) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26022 | |||
| 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 | |||
| 61900 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 59307) | https://www.ccug.se/strain?id=59307 | |||
| 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 | |
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
| 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 | |||
| 77613 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID407422.1 | StrainInfo: A central database for resolving microbial strain identifiers |