Strain identifier

BacDive ID: 8209

Type strain: Yes

Species: Perlucidibaca piscinae

Strain history: <- J.-C. Cho, Inha University, Incheon

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

@ref: 15825

BacDive-ID: 8209

DSM-Number: 21586

keywords: genome sequence, 16S sequence, Bacteria, facultative aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Perlucidibaca piscinae DSM 21586 is a facultative aerobe, mesophilic, Gram-negative bacterium that was isolated from eutrophic pond.

NCBI tax id

NCBI tax idMatching level
1122951strain
392589species

strain history

  • @ref: 15825
  • history: <- J.-C. Cho, Inha University, Incheon

doi: 10.13145/bacdive8209.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Moraxellaceae
  • genus: Perlucidibaca
  • species: Perlucidibaca piscinae
  • full scientific name: Perlucidibaca piscinae Song et al. 2008

@ref: 15825

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Moraxellaceae

genus: Perlucidibaca

species: Perlucidibaca piscinae

full scientific name: Perlucidibaca piscinae Song et al. 2008 emend. França et al. 2015

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32149negative0.95 µm0.6 µmrod-shapedyes
69480negative99.996

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_21586_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21586_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21586_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21586_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_21586_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 15825
  • 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
15825positivegrowth28mesophilic
32149positivegrowth08-37
32149positiveoptimum30mesophilic

culture pH

@refabilitytypepHPH range
32149positivegrowth06-10alkaliphile
32149positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 32149
  • oxygen tolerance: facultative aerobe

spore formation

@refspore formationconfidence
69481no100
69480no100

halophily

  • @ref: 32149
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3214922599arabinose+carbon source
3214918403L-arabitol+carbon source
3214929016arginine+carbon source
3214916947citrate+carbon source
3214928260galactose+carbon source
3214924265gluconate+carbon source
321495417glucosamine+carbon source
3214917234glucose+carbon source
3214917754glycerol+carbon source
3214915428glycine+carbon source
3214927570histidine+carbon source
3214917240itaconate+carbon source
3214915792malonate+carbon source
3214917306maltose+carbon source
3214929864mannitol+carbon source
3214937684mannose+carbon source
3214917268myo-inositol+carbon source
32149506227N-acetylglucosamine+carbon source
3214918257ornithine+carbon source
3214915361pyruvate+carbon source
3214916634raffinose+carbon source
3214926546rhamnose+carbon source
3214933942ribose+carbon source
3214917822serine+carbon source
3214930911sorbitol+carbon source
3214917992sucrose+carbon source
3214927082trehalose+carbon source
3214917151xylitol+carbon source
3214918222xylose+carbon source
3214917632nitrate+reduction

metabolite production

  • @ref: 32149
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 32149
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
32149alkaline phosphatase+3.1.3.1
32149cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 15825
  • sample type: eutrophic pond
  • geographic location: Incheon
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Pond (small)

taxonmaps

  • @ref: 69479
  • File name: preview.99_33705.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_669;96_3622;97_4450;98_24952;99_33705&stattab=map
  • Last taxonomy: Perlucidibaca piscinae
  • 16S sequence: AB681750
  • Sequence Identity:
  • Total samples: 920
  • soil counts: 74
  • aquatic counts: 511
  • animal counts: 327
  • plant counts: 8

Safety information

risk assessment

  • @ref: 15825
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Perlucidibaca piscinae gene for 16S rRNA, partial sequence, strain: NBRC 102354AB6817501450ena392589
15825Perlucidibaca piscinae strain IMCC1704 16S ribosomal RNA gene, partial sequenceDQ6642371467ena392589

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Perlucidibaca piscinae DSM 21586GCA_000420045contigncbi1122951
66792Perlucidibaca piscinae DSM 215861122951.3wgspatric1122951
66792Perlucidibaca piscinae DSM 215862524614877draftimg1122951

GC content

  • @ref: 32149
  • GC-content: 63.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.466yes
flagellatedyes57.315no
gram-positiveno98.877yes
anaerobicno99.129yes
aerobicyes85.639yes
halophileno94.316yes
spore-formingno96.151no
glucose-utilno85.458no
thermophileno98.545yes
glucose-fermentno93.046no

External links

@ref: 15825

culture collection no.: DSM 21586, KCCM 42363, NBRC 102354, IMCC 1704

straininfo link

  • @ref: 77612
  • straininfo: 399154

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18175691Perlucidibaca piscinae gen. nov., sp. nov., a freshwater bacterium belonging to the family Moraxellaceae.Song J, Choo YJ, Cho JCInt J Syst Evol Microbiol10.1099/ijs.0.65039-02008Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Fatty Acids/analysis, Fresh Water/*microbiology, Genes, rRNA, Molecular Sequence Data, Moraxellaceae/*classification/genetics/*isolation & purification/physiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny20601489Paraperlucidibaca baekdonensis gen. nov., sp. nov., isolated from seawater.Oh KH, Lee SY, Lee MH, Oh TK, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.023994-02010Base 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/analysisGenetics
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
Phylogeny28741994Perlucidibaca aquatica sp. nov., isolated from fresh water.Baek K, Han JH, Lee MHInt J Syst Evol Microbiol10.1099/ijsem.0.0019402017Bacterial Typing Techniques, Base Composition, Caves, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Moraxellaceae/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
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

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
15825Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21586)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21586
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
32149Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128392
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
77612Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399154.1StrainInfo: A central database for resolving microbial strain identifiers