Strain identifier
BacDive ID: 130462
Type strain:
Species: Paraperlucidibaca wandonensis
Strain Designation: WT-RY4
Strain history: <- KCTC <- J.-H. Yoon, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
NCBI tax ID(s): 1268273 (species)
General
@ref: 22083
BacDive-ID: 130462
DSM-Number: 29662
keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Paraperlucidibaca wandonensis WT-RY4 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from wooden branch washed ashore the sea.
NCBI tax id
- NCBI tax id: 1268273
- Matching level: species
strain history
- @ref: 22083
- history: <- KCTC <- J.-H. Yoon, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
doi: 10.13145/bacdive130462.20230509.8.1
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 wandonensis
- full scientific name: Paraperlucidibaca wandonensis Yoon et al. 2013
@ref: 22083
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Moraxellaceae
genus: Paraperlucidibaca
species: Paraperlucidibaca wandonensis
full scientific name: Paraperlucidibaca wandonensis Yoon et al. 2013
strain designation: WT-RY4
type strain: yes
Morphology
cell morphology
- @ref: 30967
- gram stain: negative
- cell length: 2.25 µm
- cell width: 0.3 µm
- cell shape: rod-shaped
- motility: yes
colony morphology
- @ref: 62981
- incubation period: 5 days
pigmentation
- @ref: 30967
- production: yes
multimedia
- @ref: 22083
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_29662.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 22083
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 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 |
---|---|---|---|---|
22083 | positive | growth | 28 | mesophilic |
30967 | positive | growth | 04-30 | |
30967 | positive | optimum | 25 | mesophilic |
62981 | positive | growth | 20 | psychrophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
30967 | positive | growth | 6.0-9.0 | alkaliphile |
30967 | positive | optimum | 7.25 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
30967 | aerobe |
62981 | aerobe |
halophily
- @ref: 30967
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-2 %
observation
- @ref: 30967
- observation: aggregates in clumps
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30967 | 30089 | acetate | + | carbon source |
30967 | 15361 | pyruvate | + | carbon source |
30967 | 17632 | nitrate | + | reduction |
enzymes
@ref | value | activity | ec |
---|---|---|---|
30967 | acid phosphatase | + | 3.1.3.2 |
30967 | alkaline phosphatase | + | 3.1.3.1 |
30967 | alpha-galactosidase | + | 3.2.1.22 |
30967 | catalase | + | 1.11.1.6 |
30967 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date |
---|---|---|---|---|---|---|
22083 | wooden branch washed ashore the sea | Wando island | Republic of Korea | KOR | Asia | |
62981 | Wood Falls | Wando | Republic of Korea | KOR | Asia | 2011 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Terrestrial | #Coast |
#Host Body-Site | #Plant | #Stem (Branch) |
#Host Body Product | #Plant | #Timber |
taxonmaps
- @ref: 69479
- File name: preview.99_81791.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_669;96_3622;97_34402;98_44352;99_81791&stattab=map
- Last taxonomy: Paraperlucidibaca wandonensis
- 16S sequence: JX994294
- Sequence Identity:
- Total samples: 822
- soil counts: 20
- aquatic counts: 675
- animal counts: 110
- plant counts: 17
Safety information
risk assessment
- @ref: 22083
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22083
- description: Paraperlucidibaca wandonensis strain WT-RY4 16S ribosomal RNA gene, partial sequence
- accession: JX994294
- length: 1459
- database: ena
- NCBI tax ID: 1268273
GC content
- @ref: 22083
- GC-content: 52.4
External links
@ref: 22083
culture collection no.: DSM 29662, CCUG 63419, KCTC 32216
straininfo link
- @ref: 88991
- straininfo: 402278
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
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 | 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 | |||
22083 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29662 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29662) | |||
30967 | 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 | 27297 | 28776041 | |
62981 | Curators of the CCUG | https://www.ccug.se/strain?id=63419 | Culture Collection University of Gothenburg (CCUG) (CCUG 63419) | |||
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/ | |||
88991 | 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-ID402278.1 |