Strain identifier

BacDive ID: 7227

Type strain: Yes

Species: Pleomorphomonas koreensis

Strain Designation: Y9

Variant: Isotype of BacDive ID 24178

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 1122962 (strain), 257440 (species)

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General

@ref: 16688

BacDive-ID: 7227

DSM-Number: 23070

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

description: Pleomorphomonas koreensis Y9 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from contaminated culture of Rhodopseudomonas palustris.

NCBI tax id

NCBI tax idMatching level
1122962strain
257440species

strain history

@refhistory
16688<- KCTC <- W.-T. Im et al., KAIST
67771<- ST Lee, KAIST

doi: 10.13145/bacdive7227.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Pleomorphomonadaceae
  • genus: Pleomorphomonas
  • species: Pleomorphomonas koreensis
  • full scientific name: Pleomorphomonas koreensis Im et al. 2006

@ref: 16688

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Pleomorphomonadaceae

genus: Pleomorphomonas

species: Pleomorphomonas koreensis

full scientific name: Pleomorphomonas koreensis Im et al. 2006

strain designation: Y9

variant: Isotype of BacDive ID 24178

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31419negative1.5-3 µm0.3-0.5 µmrod-shapedno
67771negative
69480yes92.924
69480negative99.987

pigmentation

  • @ref: 31419
  • production: yes

multimedia

  • @ref: 16688
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_23070.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 16688
  • 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
16688positivegrowth28mesophilic
31419positivegrowth15-42
31419positiveoptimum30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
31419positivegrowth06-08
31419positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31419aerobe
67771aerobe

spore formation

@refspore formationconfidence
31419no
69481no100
69480no99.976

observation

@refobservation
31419aggregates in chains
67771quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3141928757fructose+carbon source
3141933984fucose+carbon source
3141917234glucose+carbon source
3141929864mannitol+carbon source
3141937684mannose+carbon source
3141928053melibiose+carbon source
31419506227N-acetylglucosamine+carbon source
3141926546rhamnose+carbon source
3141933942ribose+carbon source
3141930911sorbitol+carbon source
3141917992sucrose+carbon source
3141917632nitrate+reduction

enzymes

@refvalueactivityec
31419catalase+1.11.1.6
31419cytochrome oxidase+1.9.3.1
31419urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
16688contaminated culture of Rhodopseudomonas palustrisRhodopseudomonas palustrisDaejeonRepublic of KoreaKORAsia
67771From small pond in KAISTRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Engineered#Laboratory
#Host#Microbial#Bacteria

taxonmaps

  • @ref: 69479
  • File name: preview.99_3678.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_1902;97_2285;98_2811;99_3678&stattab=map
  • Last taxonomy: Pleomorphomonas koreensis
  • 16S sequence: AB681245
  • Sequence Identity:
  • Total samples: 976
  • soil counts: 291
  • aquatic counts: 421
  • animal counts: 64
  • plant counts: 200

Safety information

risk assessment

  • @ref: 16688
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pleomorphomonas koreensis gene for 16S rRNA, partial sequence, strain: NBRC 100803AB6812451409ena257440
16688Pleomorphomonas koreensis gene for 16S rRNA, partial sequence, strain: Y9AB1279721417ena257440

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pleomorphomonas koreensis DSM 23070GCA_000425185scaffoldncbi1122962
66792Pleomorphomonas koreensis DSM 230701122962.3wgspatric1122962
66792Pleomorphomonas koreensis DSM 230702523533619draftimg1122962

GC content

@refGC-contentmethod
1668865.1high performance liquid chromatography (HPLC)
3141965.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes84.36no
flagellatedno82.283yes
gram-positiveno98.272no
anaerobicno93.893yes
aerobicno76.281no
halophileno96.578no
spore-formingno93.421yes
thermophileno98.004yes
glucose-utilyes88.884yes
glucose-fermentno82.341no

External links

@ref: 16688

culture collection no.: DSM 23070, KCTC 12246, NBRC 100803

straininfo link

  • @ref: 76679
  • straininfo: 232784

literature

  • topic: Phylogeny
  • Pubmed-ID: 16825646
  • title: Pleomorphomonas koreensis sp. nov., a nitrogen-fixing species in the order Rhizobiales.
  • authors: Im WT, Kim SH, Kim MK, Ten LN, Lee ST
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63499-0
  • year: 2006
  • mesh: Alphaproteobacteria/*classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA/genetics, Molecular Sequence Data, *Nitrogen Fixation, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis/chemistry, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
16688Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23070)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23070
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
31419Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127726
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
76679Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232784.1StrainInfo: A central database for resolving microbial strain identifiers