Strain identifier

BacDive ID: 130609

Type strain: Yes

Species: Yoonia sediminilitoris

Strain Designation: D1-W3

Strain history: <- CECT <- J. H. Yoon, Sungkyunkwan Univ., Suwon, Republic of Korea

NCBI tax ID(s): 1286148 (species)

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General

@ref: 21636

BacDive-ID: 130609

DSM-Number: 29955

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

description: Yoonia sediminilitoris D1-W3 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from tidal flat sediment.

NCBI tax id

  • NCBI tax id: 1286148
  • Matching level: species

strain history

  • @ref: 21636
  • history: <- CECT <- J. H. Yoon, Sungkyunkwan Univ., Suwon, Republic of Korea

doi: 10.13145/bacdive130609.20230509.8.1

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 sediminilitoris
  • full scientific name: Yoonia sediminilitoris (Park et al. 2013) Wirth and Whitman 2018

  • synonyms

    • @ref: 20215
    • synonym: Loktanella sediminilitoris

@ref: 21636

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Yoonia

species: Yoonia sediminilitoris

full scientific name: Yoonia sediminilitoris (Park et al. 2013) Wirth and Whitman 2018

strain designation: D1-W3

type strain: yes

Morphology

cell morphology

  • @ref: 31016
  • gram stain: negative
  • cell length: 2.45 µm
  • cell width: 0.6 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 21636
  • incubation period: 2-3 days

pigmentation

  • @ref: 31016
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21636
  • 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
21636positivegrowth30mesophilic
31016positivegrowth10-35
31016positiveoptimum25mesophilic

culture pH

@refabilitytypepH
31016positivegrowth5.5-8.0
31016positiveoptimum7.5

Physiology and metabolism

spore formation

  • @ref: 31016
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31016NaClpositivegrowth0-5 %
31016NaClpositiveoptimum2 %

observation

  • @ref: 31016
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3101630089acetate+carbon source
3101622599arabinose+carbon source
3101617057cellobiose+carbon source
3101628757fructose+carbon source
3101628260galactose+carbon source
3101617234glucose+carbon source
3101625115malate+carbon source
3101637684mannose+carbon source
3101617992sucrose+carbon source
3101618222xylose+carbon source
310164853esculin+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
21636catalase+1.11.1.6
21636cytochrome-c oxidase+1.9.3.1
31016alkaline phosphatase+3.1.3.1
31016catalase+1.11.1.6
31016cytochrome 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
21636-----+-+------------

Isolation, sampling and environmental information

isolation

  • @ref: 21636
  • sample type: tidal flat sediment
  • geographic location: South Sea, Boseong
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Tidal flat
#Environmental#Terrestrial#Sediment

Safety information

risk assessment

  • @ref: 21636
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21636
  • description: Loktanella sediminilitoris strain D1-W3 16S ribosomal RNA gene, partial sequence
  • accession: KC311338
  • length: 1384
  • database: ena
  • NCBI tax ID: 1286148

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Yoonia sediminilitoris DSM 29955GCA_003058085scaffoldncbi1286148
66792Yoonia sediminilitoris CECT 8284GCA_003337495scaffoldncbi1286148
66792Loktanella sediminilitoris strain DSM 299551286148.4wgspatric1286148
66792Yoonia sediminilitoris strain CECT 82841286148.5wgspatric1286148
66792Yoonia sediminilitoris CECT 82842770939487draftimg1286148
66792Yoonia sediminilitoris DSM 299552734482292draftimg1286148

GC content

  • @ref: 21636
  • GC-content: 58.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno86.148yes
gram-positiveno98.353yes
anaerobicno96.779no
halophileyes68.629no
spore-formingno95.565yes
glucose-utilyes84.273no
aerobicyes82.333no
motileno56.853no
glucose-fermentno88.73yes
thermophileno97.457yes

External links

@ref: 21636

culture collection no.: DSM 29955, CECT 8284, KCTC 32383

straininfo link

  • @ref: 89123
  • straininfo: 391313

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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

@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
21636Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29955Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29955)
31016Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172734628776041
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
89123Reimer, 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-ID391313.1