Strain identifier

BacDive ID: 13732

Type strain: Yes

Species: Leisingera daeponensis

Strain Designation: TF-218

Strain history: CIP <- 2007, JCM <- 2006, J. H. Yoon, KRIBB, Korea: strain TF-218

NCBI tax ID(s): 999547 (strain), 405746 (species)

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General

@ref: 17260

BacDive-ID: 13732

DSM-Number: 23529

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, motile, ovoid-shaped

description: Leisingera daeponensis TF-218 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from tidal flat sediment.

NCBI tax id

NCBI tax idMatching level
405746species
999547strain

strain history

@refhistory
17260<- KCTC <- J.-H. Yoon, Korea Res. Inst. Biosci. & Biotechnol. (KRIBB), Taejon, South Korea
67770J.-H. Yoon TF-218.
67771<- JH Yoon, KRIBB
118848CIP <- 2007, JCM <- 2006, J. H. Yoon, KRIBB, Korea: strain TF-218

doi: 10.13145/bacdive13732.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Leisingera
  • species: Leisingera daeponensis
  • full scientific name: Leisingera daeponensis (Yoon et al. 2007) Breider et al. 2014

  • synonyms

    • @ref: 20215
    • synonym: Phaeobacter daeponensis

@ref: 17260

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Leisingera

species: Leisingera daeponensis

full scientific name: Leisingera daeponensis (Yoon et al. 2007) Breider et al. 2014

strain designation: TF-218

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31996negative1.35 µm0.65 µmovoid-shapedyes
67771negative
69480negative99.998
118848negativerod-shapedno

colony morphology

  • @ref: 17260
  • incubation period: 3-7 days

pigmentation

  • @ref: 31996
  • production: no

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_23529_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17260BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
36607Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
118848CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
17260positivegrowth37mesophilic
31996positivegrowth04-42
31996positiveoptimum37mesophilic
36607positivegrowth37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

culture pH

@refabilitytypepH
31996positivegrowth5.5-8
31996positiveoptimum07-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31996anaerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
31996NaClpositivegrowth01-08 %
31996NaClpositiveoptimum2 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3199630089acetate+carbon source
3199616947citrate+carbon source
3199625017leucine+carbon source
3199625115malate+carbon source
3199615361pyruvate+carbon source
3199633942ribose+carbon source
3199617822serine+carbon source
3199630031succinate+carbon source
3199617632nitrate+reduction
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose-fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
11884817632nitrate-reduction
11884816301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
11884835581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
17260catalase+1.11.1.6
17260cytochrome-c oxidase+1.9.3.1
31996alkaline phosphatase+3.1.3.1
31996catalase+1.11.1.6
31996cytochrome oxidase+1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
118848oxidase+
118848catalase+1.11.1.6
118848urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118848-++--++---+---------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARA
17260--------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17260tidal flat sedimentDaepo Beach, Yellow SeaRepublic of KoreaKORAsia
67770Tidal flat at Daepo Beach (Yellow Sea)Republic of KoreaKORAsia
67771From gaetbulthe Yellow SeaRepublic of KoreaKORAsia
118848Environment, Tidal flatYellow seaRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1177.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_355;97_800;98_927;99_1177&stattab=map
  • Last taxonomy: Leisingera daeponensis
  • 16S sequence: DQ981486
  • Sequence Identity:
  • Total samples: 433
  • soil counts: 14
  • aquatic counts: 371
  • animal counts: 43
  • plant counts: 5

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
172601Risk group (German classification)
1188481Risk group (French classification)

Sequence information

16S sequences

  • @ref: 17260
  • description: Phaeobacter daeponensis strain TF-218 16S ribosomal RNA gene, partial sequence
  • accession: DQ981486
  • length: 1419
  • database: ena
  • NCBI tax ID: 999547

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Phaeobacter daeponensis DSM 23529999547.5wgspatric999547
66792Leisingera daeponensis DSM 235292521172619draftimg999547
67770Leisingera daeponensis DSM 23529GCA_000473145scaffoldncbi999547

GC content

@refGC-contentmethod
1726064.9high performance liquid chromatography (HPLC)
3199664.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes82.399yes
flagellatedno72.46no
gram-positiveno98.641yes
anaerobicno98.897no
halophileyes81.723no
spore-formingno95.648no
thermophileno96.867yes
glucose-utilyes61.568no
aerobicyes94.194no
glucose-fermentno91.768yes

External links

@ref: 17260

culture collection no.: DSM 23529, JCM 13606, KCTC 12794, CECT 7309, CIP 109576, LMG 24139

straininfo link

  • @ref: 82914
  • straininfo: 302771

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17392219Phaeobacter daeponensis sp. nov., isolated from a tidal flat of the Yellow Sea in Korea.Yoon JH, Kang SJ, Lee SY, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.64779-02007DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification/physiology, Seawater/*microbiologyGenetics
Phylogeny24449788Phaeobacter aquaemixtae sp. nov., isolated from the junction between the ocean and a freshwater spring.Park S, Park DS, Bae KS, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.057646-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Ubiquinone/chemistry, *Water MicrobiologyGenetics
Genetics24501652Genome sequence of Phaeobacter daeponensis type strain (DSM 23529(T)), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis.Dogs M, Teshima H, Petersen J, Fiebig A, Chertkov O, Dalingault H, Chen A, Pati A, Goodwin LA, Chain P, Detter JC, Ivanova N, Lapidus A, Rohde M, Gronow S, Kyrpides NC, Woyke T, Simon M, Goker M, Klenk HP, Brinkhoff TStand Genomic Sci10.4056/sigs.42879622013
Phylogeny25180090Cribrihabitans neustonicus sp. nov., isolated from coastal surface seawater, and emended description of the genus Cribrihabitans Chen et al. 2014.Hameed A, Shahina M, Lin SY, Lai WA, Liu YC, Hsu YH, Young CCInt J Syst Evol Microbiol10.1099/ijs.0.066142-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Taiwan, Ubiquinone/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17260Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23529)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23529
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
31996Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2825028776041
36607Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7334
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 life28604660 35: 676-683 2017
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68368Automatically annotated from API 20E
68382Automatically annotated from API zym
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
82914Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID302771.1StrainInfo: A central database for resolving microbial strain identifiers
118848Curators of the CIPCollection of Institut Pasteur (CIP 109576)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109576