Strain identifier

BacDive ID: 130462

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refgrowthtypetemperaturerange
22083positivegrowth28mesophilic
30967positivegrowth04-30
30967positiveoptimum25mesophilic
62981positivegrowth20psychrophilic

culture pH

@refabilitytypepHPH range
30967positivegrowth6.0-9.0alkaliphile
30967positiveoptimum7.25

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30967aerobe
62981aerobe

halophily

  • @ref: 30967
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-2 %

observation

  • @ref: 30967
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3096730089acetate+carbon source
3096715361pyruvate+carbon source
3096717632nitrate+reduction

enzymes

@refvalueactivityec
30967acid phosphatase+3.1.3.2
30967alkaline phosphatase+3.1.3.1
30967alpha-galactosidase+3.2.1.22
30967catalase+1.11.1.6
30967cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
22083wooden branch washed ashore the seaWando islandRepublic of KoreaKORAsia
62981Wood FallsWandoRepublic of KoreaKORAsia2011

isolation source categories

Cat1Cat2Cat3
#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

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23749278Paraperlucidibaca 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 KCInt J Syst Evol Microbiol10.1099/ijs.0.048645-02013Bacterial 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 MicrobiologyGenetics
Phylogeny30783797Amnimonas aquatica gen. nov., sp. nov., Isolated from a Freshwater River.Lee Y, Park HY, Jeon COCurr Microbiol10.1007/s00284-019-01652-52019Base 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 MicrobiologyPhenotype

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
22083Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29662Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29662)
30967Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172729728776041
62981Curators of the CCUGhttps://www.ccug.se/strain?id=63419Culture Collection University of Gothenburg (CCUG) (CCUG 63419)
69479João 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 betahttps://microbeatlas.org/
88991Reimer, 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 identifiers10.60712/SI-ID402278.1