Strain identifier

BacDive ID: 24517

Type strain: Yes

Species: Seohaeicola saemankumensis

Strain Designation: SD-15

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 481181 (species)

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General

@ref: 21202

BacDive-ID: 24517

DSM-Number: 28224

keywords: 16S sequence, Bacteria, anaerobe, Gram-negative

description: Seohaeicola saemankumensis SD-15 is an anaerobe, Gram-negative bacterium that was isolated from tidal flat.

NCBI tax id

  • NCBI tax id: 481181
  • Matching level: species

strain history

@refhistory
21202<- KCTC <- J.-H. Yoon, KRIBB; SD-15
67771<- JH Yoon, KRIBB

doi: 10.13145/bacdive24517.20240510.9

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Seohaeicola
  • species: Seohaeicola saemankumensis
  • full scientific name: Seohaeicola saemankumensis Yoon et al. 2009

@ref: 21202

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Seohaeicola

species: Seohaeicola saemankumensis

full scientific name: Seohaeicola saemankumensis Yoon et al. 2009

strain designation: SD-15

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotility
29347negative5.5 µm1.25 µmno
67771negative

colony morphology

  • @ref: 21202
  • incubation period: 3-7 days

pigmentation

  • @ref: 29347
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21202
  • 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

@refgrowthtypetemperature
21202positivegrowth25
29347positivegrowth04-40
29347positiveoptimum30
67771positivegrowth30

culture pH

@refabilitytypepH
29347positivegrowth5.5-8
29347positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29347anaerobe
67771aerobe

halophily

@refsaltgrowthtested relationconcentration
29347NaClpositivegrowth01-07 %
29347NaClpositiveoptimum2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2934730089acetate+carbon source
2934725115malate+carbon source
2934737684mannose+carbon source
2934730031succinate+carbon source
2934717632nitrate+reduction
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-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
21202catalase+1.11.1.6
21202cytochrome-c 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
21202+---+----+/-----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
21202tidal flatSaemankum, Yellow SeaRepublic of KoreaKORAsia
60530Tidal flat sedimentSaemankum,Yellow SeaRepublic of KoreaKORAsia2005
67771From tidal flatSaemankum, the Yellow SeaRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Tidal flat

taxonmaps

  • @ref: 69479
  • File name: preview.99_3349.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1749;97_2091;98_2568;99_3349&stattab=map
  • Last taxonomy: Seohaeicola saemankumensis subclade
  • 16S sequence: EU221274
  • Sequence Identity:
  • Total samples: 4411
  • soil counts: 298
  • aquatic counts: 3567
  • animal counts: 486
  • plant counts: 60

Safety information

risk assessment

  • @ref: 21202
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21202
  • description: Seohaeicola saemankumensis strain SD-15 16S ribosomal RNA gene, partial sequence
  • accession: EU221274
  • length: 1422
  • database: nuccore
  • NCBI tax ID: 481181

GC content

  • @ref: 29347
  • GC-content: 63.4

External links

@ref: 21202

culture collection no.: DSM 28224, CCUG 55328, KCTC 22175

straininfo link

  • @ref: 88372
  • straininfo: 398381

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19625441Seohaeicola saemankumensis gen. nov., sp. nov., isolated from a tidal flat.Yoon JH, Kang SJ, Lee SY, Oh KH, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.011312-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/classification/genetics/*isolation & purification/metabolism, Seawater/*microbiologyMetabolism
Phylogeny24585075Seohaeicola westpacificensis sp. nov., a novel member of genera Seohaeicola isolated from deep West Pacific Sea water.Xian S, Zhang R, Sun J, Chen Y, Deng W, Li S, Jiao NCurr Microbiol10.1007/s00284-014-0548-12014Bacterial Typing Techniques, Base Composition, Base Sequence, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Molecular Sequence Data, Pacific Ocean, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification/physiology, Seawater/microbiology, Sequence Analysis, DNAGenetics
Phylogeny25027448Seohaeicola nanhaiensis sp. nov., a moderately halophilic bacterium isolated from the benthic sediment of South China Sea.Xie BS, Lv XL, Cai M, Tang YQ, Wang YN, Cui HL, Liu XY, Tan Y, Wu XLCurr Microbiol10.1007/s00284-014-0658-92014Aerobiosis, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureGenetics

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
21202Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28224Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28224)
29347Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172575928776041
60530Curators of the CCUGhttps://www.ccug.se/strain?id=55328Culture Collection University of Gothenburg (CCUG) (CCUG 55328)
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
88372Reimer, 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-ID398381.1