Strain identifier

BacDive ID: 3810

Type strain: Yes

Species: Hymenobacter daecheongensis

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 1121955 (strain), 496053 (species)

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General

@ref: 15542

BacDive-ID: 3810

DSM-Number: 21074

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

description: Hymenobacter daecheongensis DSM 21074 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from stream sediment.

NCBI tax id

NCBI tax idMatching level
1121955strain
496053species

strain history

@refhistory
15542<- S.-T. Lee, KAIST <- W.-T. Im; Dae14
67771<- ST Lee, KAIST

doi: 10.13145/bacdive3810.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Hymenobacteraceae
  • genus: Hymenobacter
  • species: Hymenobacter daecheongensis
  • full scientific name: Hymenobacter daecheongensis Xu et al. 2009

@ref: 15542

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Hymenobacteraceae

genus: Hymenobacter

species: Hymenobacter daecheongensis

full scientific name: Hymenobacter daecheongensis Xu et al. 2009

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
28950negative3.5 µm0.8 µmrod-shapedno
67771rod-shapedno
67771negative
69480negative99.998

pigmentation

  • @ref: 28950
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 15542
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
15542positivegrowth30mesophilic
28950positivegrowth04-30
28950positiveoptimum17psychrophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
28950positivegrowth05-10alkaliphile
28950positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
28950aerobe
67771aerobe

spore formation

@refspore formationconfidence
28950no
67771no
69481no100
69480no99.997

halophily

  • @ref: 28950
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <1 %

observation

@refobservation
28950aggregates in clumps
67771quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
28950161933-hydroxybenzoate+carbon source
28950370543-hydroxybutyrate+carbon source
2895030089acetate+carbon source
2895017128adipate+carbon source
2895015963ribitol+carbon source
2895022599arabinose+carbon source
2895027689decanoate+carbon source
2895016947citrate+carbon source
2895015740formate+carbon source
2895028260galactose+carbon source
2895017754glycerol+carbon source
2895028087glycogen+carbon source
2895027570histidine+carbon source
2895017240itaconate+carbon source
2895024996lactate+carbon source
2895017716lactose+carbon source
2895025115malate+carbon source
2895015792malonate+carbon source
2895029864mannitol+carbon source
28950506227N-acetylglucosamine+carbon source
2895018401phenylacetate+carbon source
2895026271proline+carbon source
2895017272propionate+carbon source
2895016634raffinose+carbon source
2895017814salicin+carbon source
2895030911sorbitol+carbon source
289509300suberic acid+carbon source
2895030031succinate+carbon source
2895031011valerate+carbon source
2895017151xylitol+carbon source
2895018222xylose+carbon source

enzymes

@refvalueactivityec
28950acid phosphatase+3.1.3.2
28950alkaline phosphatase+3.1.3.1
28950catalase+1.11.1.6
28950gelatinase+
28950cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15542stream sedimentnear Daecheong DamRepublic of KoreaKORAsia
67771From stream sediment near Daecheong DamRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2689.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_263;96_1433;97_1710;98_2086;99_2689&stattab=map
  • Last taxonomy: Hymenobacter daecheongensis subclade
  • 16S sequence: EU370958
  • Sequence Identity:
  • Total samples: 588
  • soil counts: 112
  • aquatic counts: 137
  • animal counts: 325
  • plant counts: 14

Safety information

risk assessment

  • @ref: 15542
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15542
  • description: Hymenobacter daecheongensis strain Dae14 16S ribosomal RNA gene, partial sequence
  • accession: EU370958
  • length: 1468
  • database: ena
  • NCBI tax ID: 496053

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hymenobacter daecheongensis DSM 21074GCA_900141805contigncbi1121955
66792Hymenobacter daecheongensis DSM 210741121955.3wgspatric1121955
66792Hymenobacter daecheongensis DSM 210742582581872draftimg1121955

GC content

@refGC-contentmethod
1554262.2high performance liquid chromatography (HPLC)
2895062.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.056no
flagellatedno96.964yes
gram-positiveno97.501yes
anaerobicno99.032yes
halophileno94.293yes
spore-formingno93.98yes
thermophileno97.6yes
glucose-utilyes71.408no
aerobicyes89.789yes
glucose-fermentno91.502no

External links

@ref: 15542

culture collection no.: DSM 21074, KCTC 22258, LMG 24498, Dae 14

straininfo link

  • @ref: 73321
  • straininfo: 339818

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19406816Hymenobacter daecheongensis sp. nov., isolated from stream sediment.Xu JL, Liu QM, Yu HS, Jin FX, Lee ST, Im WTInt J Syst Evol Microbiol10.1099/ijs.0.002444-02009Bacterial Typing Techniques, Cytophagaceae/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny29934694Description of Hymenobacter daejeonensis sp. nov., isolated from grass soil, based on multilocus sequence analysis of the 16S rRNA gene, gyrB and tuf genes.Jin L, Wu X, Ko SR, Jin FJ, Li T, Ahn CY, Oh HM, Lee HGAntonie Van Leeuwenhoek10.1007/s10482-018-1119-42018Base Composition, Cytophagaceae/classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Multilocus Sequence Typing, Phylogeny, Poaceae/growth & development, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism
Phylogeny31823137Hymenobacter jejuensis sp. nov., a UV radiation-tolerant bacterium isolated from Jeju Island.Maeng S, Kim MK, Subramani GAntonie Van Leeuwenhoek10.1007/s10482-019-01363-82019Bacteroidetes/*classification/*genetics/radiation effects, Genome, Bacterial, Islands, Phylogeny, Republic of Korea, *Soil Microbiology, *Ultraviolet RaysGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15542Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21074)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21074
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
28950Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2538928776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
73321Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID339818.1StrainInfo: A central database for resolving microbial strain identifiers