Strain identifier

BacDive ID: 5590

Type strain: Yes

Species: Gaetbulibacter saemankumensis

Strain Designation: SMK-12

Strain history: CIP <- 2005, KCTC <- JH Yoon, KRIBB

NCBI tax ID(s): 1121909 (strain), 311208 (species)

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General

@ref: 6696

BacDive-ID: 5590

DSM-Number: 17032

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

description: Gaetbulibacter saemankumensis SMK-12 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from tidal flat.

NCBI tax id

NCBI tax idMatching level
1121909strain
311208species

strain history

@refhistory
6696<- J.-H. Yoon <- S.-Y. Jung; SMK-12 {2004}
67770J.-H. Yoon SMK-12.
67771<- JH Yoon, KRIBB
122344CIP <- 2005, KCTC <- JH Yoon, KRIBB

doi: 10.13145/bacdive5590.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Gaetbulibacter
  • species: Gaetbulibacter saemankumensis
  • full scientific name: Gaetbulibacter saemankumensis Jung et al. 2005

@ref: 6696

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Gaetbulibacter

species: Gaetbulibacter saemankumensis

full scientific name: Gaetbulibacter saemankumensis Jung et al. 2005

strain designation: SMK-12

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
31523negative3.75 µm0.45 µmrod-shapedyesgliding
67771rod-shapedyesgliding
67771negative
69480negative99.98

pigmentation

  • @ref: 31523
  • production: no

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_17032_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17032_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17032_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17032_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17032_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6696BACTO 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
37404Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
122344CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6696positivegrowth28mesophilic
31523positivegrowth13-40
31523positiveoptimum27mesophilic
37404positivegrowth30mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
31523positivegrowth5.5-8.0
31523positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6696aerobe
31523aerobe
67771aerobe

spore formation

@refspore formationconfidence
31523no
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
31523NaClpositivegrowth02-07 %
31523NaClpositiveoptimum3.5 %

observation

@refobservation
67770quinones: MK-6
67771quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3152317057cellobiose+carbon source
3152328757fructose+carbon source
3152328260galactose+carbon source
3152317234glucose+carbon source
3152317716lactose+carbon source
3152317306maltose+carbon source
3152326271proline+carbon source
3152326546rhamnose+carbon source
3152317992sucrose+carbon source
3152318222xylose+carbon source
315234853esculin+hydrolysis
3152317632nitrate+reduction

enzymes

@refvalueactivityec
31523acid phosphatase+3.1.3.2
31523alkaline phosphatase+3.1.3.1
31523catalase+1.11.1.6
31523cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
6696tidal flatRepublic of KoreaKORAsia
67770Tidal flat sediment at SaemankumRepublic of KoreaKORAsiaPyunsan
67771From tidal flat sedimentRepublic of KoreaKORAsiaSaemankum, Pyunsan, the Yellow Sea
122344Environment, Tidal flat sediment of the Yellow SeaRepublic of KoreaKORAsiaYellow Sea

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_7856.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_107;96_3640;97_4474;98_5740;99_7856&stattab=map
  • Last taxonomy: Gaetbulibacter saemankumensis subclade
  • 16S sequence: AY883937
  • Sequence Identity:
  • Total samples: 90
  • soil counts: 6
  • aquatic counts: 84

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
66961Risk group (German classification)
1223441Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6696
  • description: Gaetbulibacter saemankumensis strain SMK-12 16S ribosomal RNA gene, partial sequence
  • accession: AY883937
  • length: 1474
  • database: ena
  • NCBI tax ID: 311208

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gaetbulibacter saemankumensis DSM 170321121909.4wgspatric1121909
66792Gaetbulibacter saemankumensis DSM 170322524614665draftimg1121909
67770Gaetbulibacter saemankumensis DSM 17032GCA_000425645scaffoldncbi1121909

GC content

@refGC-contentmethod
6777034.8high performance liquid chromatography (HPLC)
6777134.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.712no
flagellatedno94.691no
gram-positiveno98.172yes
anaerobicno99.403yes
halophileno73.829no
spore-formingno97.307yes
thermophileno98.398yes
glucose-utilyes87.378yes
aerobicyes79.623no
glucose-fermentno89.48no

External links

@ref: 6696

culture collection no.: DSM 17032, KCTC 12379, JCM 12931, IAM 15373, CIP 108967

straininfo link

  • @ref: 75072
  • straininfo: 265598

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16166676Gaetbulibacter saemankumensis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a tidal flat sediment in Korea.Jung SY, Kang SJ, Lee MH, Lee SY, Oh TK, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.63738-02005Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification/physiology, Genes, rRNA, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNAGenetics
Phylogeny18218924Gaetbulibacter marinus sp. nov., isolated from coastal seawater, and emended description of the genus Gaetbulibacter.Yang SJ, Cho JCInt J Syst Evol Microbiol10.1099/ijs.0.65382-02008Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Fatty Acids/analysis, Flavobacteriaceae/chemistry/*classification/genetics/*isolation & purification, Genes, rRNA, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny21357459Gaetbulibacter aestuarii sp. nov., isolated from shallow coastal seawater, and emended description of the genus Gaetbulibacter.Park SC, Choe HN, Baik KS, Lee KH, Seong CNInt J Syst Evol Microbiol10.1099/ijs.0.028944-02011Aerobiosis, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Oxidoreductases/metabolism, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNAMetabolism
Phylogeny22685106Gaetbulibacter lutimaris sp. nov., isolated from a tidal flat sediment.Yoon JH, Lee SY, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.040352-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny26669721Gaetbulibacter aquiaggeris sp. nov., a member of the Flavobacteriaceae isolated from seawater.Jung YT, Lee JS, Yoon JHInt J Syst Evol Microbiol10.1099/ijsem.0.0008452015

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6696Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17032)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17032
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
31523Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2781728776041
37404Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6655
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
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
75072Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265598.1StrainInfo: A central database for resolving microbial strain identifiers
122344Curators of the CIPCollection of Institut Pasteur (CIP 108967)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108967