Strain identifier

BacDive ID: 130607

Type strain: Yes

Species: Yoonia litorea

Strain Designation: DPG-5

Strain history: <- KCTC <- J.-H. Yoon, KRIBB; DPG-5

NCBI tax ID(s): 1123755 (species)

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General

@ref: 21634

BacDive-ID: 130607

DSM-Number: 29433

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

description: Yoonia litorea DPG-5 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 1123755
  • Matching level: species

strain history

  • @ref: 21634
  • history: <- KCTC <- J.-H. Yoon, KRIBB; DPG-5

doi: 10.13145/bacdive130607.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Yoonia
  • species: Yoonia litorea
  • full scientific name: Yoonia litorea (Yoon et al. 2013) Wirth and Whitman 2018

  • synonyms

    • @ref: 20215
    • synonym: Loktanella litorea

@ref: 21634

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Yoonia

species: Yoonia litorea

full scientific name: Yoonia litorea (Yoon et al. 2013) Wirth and Whitman 2018

strain designation: DPG-5

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30581negative3.15 µm0.6 µmrod-shapedno
69480negative99.987

colony morphology

@refincubation period
216342-3 days
627853 days

pigmentation

  • @ref: 30581
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21634
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
21634positivegrowth30mesophilic
30581positivegrowth15-37
30581positiveoptimum30mesophilic
62785positivegrowth30mesophilic

culture pH

@refabilitytypepH
30581positivegrowth06-08
30581positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30581aerobe
62785aerobe

spore formation

@refspore formationconfidence
30581no
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
30581NaClpositivegrowth01-07 %
30581NaClpositiveoptimum2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3058130089acetate+carbon source
3058117057cellobiose+carbon source
3058128260galactose+carbon source
3058117234glucose+carbon source
3058125115malate+carbon source
3058117306maltose+carbon source
3058137684mannose+carbon source
3058115361pyruvate+carbon source
3058130031succinate+carbon source
3058117992sucrose+carbon source
3058127082trehalose+carbon source
305814853esculin+hydrolysis
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
21634catalase+1.11.1.6
21634cytochrome-c oxidase+1.9.3.1
30581alkaline phosphatase+3.1.3.1
30581catalase+1.11.1.6
30581cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
21634-----+-+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
21634seawaterSouth Sea, GeojedoRepublic of KoreaKORAsia
62785SeawaterSouth Sea,GeojedoRepublic of KoreaKORAsia2008

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_27806.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_683;97_4481;98_5749;99_27806&stattab=map
  • Last taxonomy: Yoonia litorea
  • 16S sequence: JN885197
  • Sequence Identity:
  • Total samples: 552
  • soil counts: 4
  • aquatic counts: 527
  • animal counts: 6
  • plant counts: 15

Safety information

risk assessment

  • @ref: 21634
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21634
  • description: Loktanella litorea strain DPG-5 16S ribosomal RNA gene, partial sequence
  • accession: JN885197
  • length: 1384
  • database: ena
  • NCBI tax ID: 1123755

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Yoonia litorea DSM 29433GCA_900114675contigncbi1123755
66792Yoonia litorea strain DSM 294331123755.5wgspatric1123755
66792Yoonia litorea DSM 294332687453745draftimg1123755

GC content

@refGC-contentmethod
3058157.6
2163457.6high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno57.79yes
flagellatedno79.883no
gram-positiveno97.697no
anaerobicno97.654no
aerobicyes87.128no
halophileyes79.436no
spore-formingno94.673yes
thermophileno92.204no
glucose-utilyes61.754no
glucose-fermentno90.838yes

External links

@ref: 21634

culture collection no.: DSM 29433, CCUG 62113, KCTC 23883

straininfo link

  • @ref: 89121
  • straininfo: 401932

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22389278Loktanella litorea sp. nov., isolated from seawater.Yoon JH, Jung YT, Lee JSInt J Syst Evol Microbiol10.1099/ijs.0.039198-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/analysis, *Water MicrobiologyGenetics
Phylogeny25428418Loktanella sediminum sp. nov., isolated from marine surface sediment.Liang J, Zhang Z, Liu Y, Wang M, Zhang XHInt J Syst Evol Microbiol10.1099/ijs.0.070680-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryGenetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
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
21634Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29433Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29433)
30581Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172691228776041
62785Curators of the CCUGhttps://www.ccug.se/strain?id=62113Culture Collection University of Gothenburg (CCUG) (CCUG 62113)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
68369Automatically annotated from API 20NE
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
89121Reimer, 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-ID401932.1