Strain identifier

BacDive ID: 24510

Type strain: Yes

Species: Donghicola eburneus

Strain Designation: SW-277

Strain history: CIP <- 2007, JCM <- 2006, J.H. Yoon, KRIBB, Taejon, Korea: strain SW-277

NCBI tax ID(s): 393278 (species)

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

@ref: 21156

BacDive-ID: 24510

DSM-Number: 29127

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

description: Donghicola eburneus SW-277 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater sample.

NCBI tax id

  • NCBI tax id: 393278
  • Matching level: species

strain history

@refhistory
21156<- JCM <- J. H. Yoon, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea; SW-277
67770J.-H. Yoon SW-277.
67771<- JH Yoon, KRIBB
118991CIP <- 2007, JCM <- 2006, J.H. Yoon, KRIBB, Taejon, Korea: strain SW-277

doi: 10.13145/bacdive24510.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Donghicola
  • species: Donghicola eburneus
  • full scientific name: Donghicola eburneus Yoon et al. 2007

@ref: 21156

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Donghicola

species: Donghicola eburneus

full scientific name: Donghicola eburneus Yoon et al. 2007

strain designation: SW-277

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31875negative1.3 µm0.7 µmcoccus-shapedno
67771negative
69480negative99.995
118991negativerod-shapedno

colony morphology

  • @ref: 21156
  • incubation period: 1-2 days

pigmentation

  • @ref: 31875
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
21156BACTO 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
37752Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
118991CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
21156positivegrowth30mesophilic
31875positivegrowth10-42
31875positiveoptimum26mesophilic
37752positivegrowth37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

culture pH

@refabilitytypepH
31875positivegrowth07-08
31875positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31875aerobe
67771aerobe

spore formation

@refspore formationconfidence
31875no
69481no100
69480no99.946

halophily

@refsaltgrowthtested relationconcentration
31875NaClpositivegrowth01-12 %
31875NaClpositiveoptimum2 %

observation

@refobservation
31875aggregates in chains
67770quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3187530089acetate+carbon source
3187522599arabinose+carbon source
3187517057cellobiose+carbon source
3187528757fructose+carbon source
3187528260galactose+carbon source
3187517234glucose+carbon source
3187517716lactose+carbon source
3187525115malate+carbon source
3187517306maltose+carbon source
3187529864mannitol+carbon source
3187537684mannose+carbon source
3187515361pyruvate+carbon source
3187530911sorbitol+carbon source
3187530031succinate+carbon source
3187517992sucrose+carbon source
3187517632nitrate+reduction
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
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
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
11899117632nitrate-reduction
11899116301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11899135581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
21156catalase+1.11.1.6
21156cytochrome-c oxidase+1.9.3.1
31875catalase+1.11.1.6
31875cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369arginine dihydrolase-3.5.3.6
118991oxidase+
118991catalase+1.11.1.6
118991urease-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
118991-+++----------------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
21156+---+/-+--++++-++--++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118991------------------------+/------------------------+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
21156seawater sampleEast Sea, JongdongjinRepublic of KoreaKORAsia
67770Seawater
67771From seawaterRepublic of KoreaKORAsia
118991Environment, Sea waterEast Sea, JongdongjinRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_41959.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_11109;97_13452;98_16569;99_41959&stattab=map
  • Last taxonomy: Donghicola eburneus subclade
  • 16S sequence: DQ667965
  • Sequence Identity:
  • Total samples: 1331
  • soil counts: 13
  • aquatic counts: 1273
  • animal counts: 44
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
211561Risk group (German classification)
1189911Risk group (French classification)

Sequence information

16S sequences

  • @ref: 21156
  • description: Donghicola eburneus strain SW-277 16S ribosomal RNA gene, partial sequence
  • accession: DQ667965
  • length: 1416
  • database: ena
  • NCBI tax ID: 393278

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Donghicola eburneus strain DSM 29127393278.4wgspatric393278
66792Donghicola eburneus DSM 291272684622851draftimg393278
67770Donghicola eburneus DSM 29127GCA_900115865contigncbi393278

GC content

@refGC-contentmethod
3187559.7
2115659.7high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno99.056yes
anaerobicno98.147no
halophileyes61.364no
spore-formingno96.305yes
glucose-utilyes88.235yes
aerobicyes86.966yes
motileyes68.42no
flagellatedno71.146no
thermophileno97.911no
glucose-fermentno89.282yes

External links

@ref: 21156

culture collection no.: DSM 29127, JCM 13604, KCTC 12735, CIP 109518

straininfo link

  • @ref: 88367
  • straininfo: 297173

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17220445Donghicola eburneus gen. nov., sp. nov., isolated from seawater of the East Sea in Korea.Yoon JH, Kang SJ, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.64577-02007Alphaproteobacteria/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny19406808Donghicola xiamenensis sp. nov., a marine bacterium isolated from seawater of the Taiwan Strait in China.Tan T, Wang B, Shao ZInt J Syst Evol Microbiol10.1099/ijs.0.000901-02009Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification/physiology, Seawater/*microbiology, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny19897619Pontibaca methylaminivorans gen. nov., sp. nov., a member of the family Rhodobacteraceae.Kim KK, Lee JS, Lee KC, Oh HM, Kim SGInt J Syst Evol Microbiol10.1099/ijs.0.020172-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/metabolism, Sodium Chloride/metabolismMetabolism
Phylogeny24844264Youngimonas vesicularis gen. nov., sp. nov., of the family Rhodobacteraceae, isolated from surface seawater, reclassification of Donghicola xiamenensis Tan et al. 2009 as Pseudodonghicola xiamenensis gen. nov., comb. nov. and emended description of the genus Donghicola Yoon et al. 2007.Hameed A, Shahina M, Lin SY, Nakayan P, Liu YC, Lai WA, Hsu YHInt J Syst Evol Microbiol10.1099/ijs.0.060962-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Taiwan, Ubiquinone/chemistryGenetics
Phylogeny26311168Donghicola tyrosinivorans sp. nov., a tyrosine-degrading bacterium isolated from seawater.Sung HR, Lee JM, Kim M, Yun BR, Shin KSInt J Syst Evol Microbiol10.1099/ijsem.0.0005432015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Tyrosine/metabolism, Ubiquinone/chemistryTranscriptome
Phylogeny28840796Monaibacterium marinum, gen. nov, sp. nov, a new member of the Alphaproteobacteria isolated from seawater of Menai Straits, Wales, UK.Chernikova TN, Dallimore J, Lunsdorf H, Heipieper HJ, Golyshin PNInt J Syst Evol Microbiol10.1099/ijsem.0.0021112017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry, WalesTranscriptome
Phylogeny29160201Aquicoccus porphyridii gen. nov., sp. nov., isolated from a small marine red alga, Porphyridium marinum.Feng T, Kim KH, Jeong SE, Kim W, Jeon COInt J Syst Evol Microbiol10.1099/ijsem.0.0024982017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Porphyridium/*microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny33119482Arenibacterium halophilum gen. nov., sp. nov., a halotolerant bacterium in the family Rhodobacteraceae isolated from a coastal sand dune.Baek J, Kim JH, Yoon JH, Lee JS, Sukhoom A, Kim WInt J Syst Evol Microbiol10.1099/ijsem.0.0045342020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics, Sand/*microbiology, Seawater/microbiology, Sequence Analysis, DNA, Species SpecificityTranscriptome
Phylogeny33263508Donghicola mangrovi sp. nov., a member of the family Rhodobacteraceae isolated from mangrove forest in Thailand.Charoenyingcharoen P, Kim JS, Theeragool G, Lee KC, Yukphan P, Lee JSInt J Syst Evol Microbiol10.1099/ijsem.0.0045702020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Sequence Analysis, DNA, Thailand, Ubiquinone/analogs & derivatives/chemistry, *WetlandsTranscriptome

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
21156Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29127Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29127)
31875Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172813528776041
37752Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7271
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
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.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
88367Reimer, 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-ID297173.1
118991Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109518Collection of Institut Pasteur (CIP 109518)