Strain identifier

BacDive ID: 23225

Type strain: Yes

Species: Yoonia tamlensis

Strain Designation: SSW-35

Strain history: <- SD Lee, Cheju Univ.

NCBI tax ID(s): 390270 (species)

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

@ref: 19133

BacDive-ID: 23225

DSM-Number: 26879

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

description: Yoonia tamlensis SSW-35 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 390270
  • Matching level: species

strain history

@refhistory
19133<- JCM <- S. D. Lee; SSW-35
67770S. D. Lee SSW-35.
67771<- SD Lee, Cheju Univ.

doi: 10.13145/bacdive23225.20230509.8.1

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 tamlensis
  • full scientific name: Yoonia tamlensis (Lee 2012) Wirth and Whitman 2018
  • synonyms

    • @ref: 20215
    • synonym: Loktanella tamlensis

@ref: 19133

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Yoonia

species: Yoonia tamlensis

full scientific name: Yoonia tamlensis (Lee 2012) Wirth and Whitman 2018

strain designation: SSW-35

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30106negative1.1-1.7 µm0.7 µmrod-shapedyes
67771negative
69480negative99.993

colony morphology

  • @ref: 19133
  • incubation period: 2-3 days

pigmentation

  • @ref: 30106
  • production: no

Culture and growth conditions

culture medium

  • @ref: 19133
  • 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
19133positivegrowth30mesophilic
30106positivegrowth4-30
30106positiveoptimum25-30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
30106positivegrowth07-10alkaliphile
30106positiveoptimum07-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30106aerobe
67771aerobe

spore formation

@refspore formationconfidence
30106no
69481no100
69480no99.999

halophily

  • @ref: 30106
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 1-6 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
301064853esculin+hydrolysis
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

@refChebi-IDmetaboliteproduction
3010616136hydrogen sulfideyes
6836935581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
19133catalase+1.11.1.6
19133cytochrome-c oxidase+1.9.3.1
30106acid phosphatase+3.1.3.2
30106alkaline phosphatase+3.1.3.1
30106catalase+1.11.1.6
30106cytochrome 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
19133-----++++/---+++---+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
19133seawaterJeju, Samyang BeachRepublic of KoreaKORAsia
67770Seawater collected from Samyang Beach in JejuRepublic of KoreaKORAsia
67771From seawater in the coast of Jeju IslandRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_79986.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_683;97_4510;98_5790;99_79986&stattab=map
  • Last taxonomy: Yoonia tamlensis
  • 16S sequence: DQ533556
  • Sequence Identity:
  • Total samples: 1213
  • soil counts: 40
  • aquatic counts: 1102
  • animal counts: 18
  • plant counts: 53

Safety information

risk assessment

  • @ref: 19133
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19133
  • description: Loktanella tamlensis strain SSW-35 16S ribosomal RNA gene, partial sequence
  • accession: DQ533556
  • length: 1352
  • database: ena
  • NCBI tax ID: 390270

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Yoonia tamlensis strain DSM 26879390270.6wgspatric390270
66792Yoonia tamlensis DSM 268792619619642draftimg390270
67770Yoonia tamlensis DSM 26879GCA_900115105scaffoldncbi390270

GC content

@refGC-contentmethod
1913355.0high performance liquid chromatography (HPLC)
3010655
6777055high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno97.945no
anaerobicno98.944yes
halophileyes71.64no
spore-formingno96.338no
glucose-utilyes80.909no
aerobicyes92.926no
flagellatedno79.82no
motileyes51.422no
thermophileno98.198yes
glucose-fermentno89.759no

External links

@ref: 19133

culture collection no.: DSM 26879, JCM 14020, KCTC 12722

straininfo link

  • @ref: 87451
  • straininfo: 401340

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21515703Loktanella tamlensis sp. nov., isolated from seawater.Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.029462-02011Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, Temperature, Ubiquinone/analysisGenetics
Phylogeny23749279Loktanella sediminilitoris sp. nov., isolated from tidal flat sediment.Park S, Jung YT, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.049841-02013Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/microbiology, Ubiquinone/analogs & derivatives/chemistryGenetics
Phylogeny24744019Loktanella maritima sp. nov. isolated from shallow marine sediments.Tanaka N, Romanenko LA, Kurilenko VV, Svetashev VI, Kalinovskaya NI, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.061747-02014DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Ubiquinone/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
19133Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26879)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26879
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
30106Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2646228776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.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
87451Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401340.1StrainInfo: A central database for resolving microbial strain identifiers