Strain identifier

BacDive ID: 130271

Type strain: Yes

Species: Dyadobacter jejuensis

Strain Designation: AM1R11

Strain history: K. Y. Jahng AM1R11.

NCBI tax ID(s): 1082580 (species)

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General

@ref: 21579

BacDive-ID: 130271

DSM-Number: 100346

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

description: Dyadobacter jejuensis AM1R11 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater.

NCBI tax id

  • NCBI tax id: 1082580
  • Matching level: species

strain history

@refhistory
21579<- KACC <- J. Chun and colleagues, Chonbuk National University, Dept. of Life Sciences, Jeonju-si, Republic of Korea
67770K. Y. Jahng AM1R11.

doi: 10.13145/bacdive130271.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Spirosomataceae
  • genus: Dyadobacter
  • species: Dyadobacter jejuensis
  • full scientific name: Dyadobacter jejuensis Chun et al. 2013

@ref: 21579

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Spirosomaceae

genus: Dyadobacter

species: Dyadobacter jejuensis

full scientific name: Dyadobacter jejuensis Chun et al. 2013

strain designation: AM1R11

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30753negative2.5 µm0.85 µmrod-shapedno
69480no90.524
69480negative99.997

pigmentation

  • @ref: 30753
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21579
  • name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1a
  • composition: Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a; with strain-specific modifications) Composition: Agar 15.0 g/l NaCl 5.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
21579positivegrowth28mesophilic
30753positivegrowth15-37
30753positiveoptimum25mesophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
30753positivegrowth06-10alkaliphile
30753positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30753
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.951

halophily

  • @ref: 30753
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-3 %

observation

  • @ref: 30753
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3075340585alpha-cyclodextrin+carbon source
3075322599arabinose+carbon source
3075317057cellobiose+carbon source
3075323652dextrin+carbon source
3075328757fructose+carbon source
3075328260galactose+carbon source
3075317234glucose+carbon source
3075317716lactose+carbon source
3075317306maltose+carbon source
3075329864mannitol+carbon source
3075337684mannose+carbon source
3075328053melibiose+carbon source
3075337657methyl D-glucoside+carbon source
3075316634raffinose+carbon source
3075330031succinate+carbon source
3075317992sucrose+carbon source
3075327082trehalose+carbon source
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
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
30753alpha-galactosidase+3.2.1.22
30753catalase+1.11.1.6
30753cytochrome oxidase+1.9.3.1
68369cytochrome 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_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
21579-----+-++-++++------+
21579-----+-++-++++------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
21579seawatersouth coast of Jeju IslandRepublic of KoreaKORAsia
67770Seawater of Jeju IslandRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_34147.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_496;96_2473;97_3018;98_3786;99_34147&stattab=map
  • Last taxonomy: Dyadobacter jejuensis
  • 16S sequence: JN597283
  • Sequence Identity:
  • Total samples: 80
  • aquatic counts: 67
  • animal counts: 10
  • plant counts: 3

Safety information

risk assessment

  • @ref: 21579
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21579
  • description: Dyadobacter jejuensis strain AM1R11 16S ribosomal RNA gene, partial sequence
  • accession: JN597283
  • length: 1346
  • database: ena
  • NCBI tax ID: 1082580

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dyadobacter jejuensis strain DSM 1003461082580.3wgspatric1082580
66792Dyadobacter jejuensis DSM 1003462731639220draftimg1082580
67770Dyadobacter jejuensis DSM 100346GCA_003149085scaffoldncbi1082580

GC content

  • @ref: 30753
  • GC-content: 45.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.465no
flagellatedno97.09no
gram-positiveno98.063no
anaerobicno99.038yes
aerobicyes93.315yes
halophileno94.032no
spore-formingno96.189no
thermophileno99.431no
glucose-utilyes88.364yes
glucose-fermentno87.328yes

External links

@ref: 21579

culture collection no.: DSM 100346, JCM 17918, KACC 16446

straininfo link

  • @ref: 88808
  • straininfo: 403464

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22962334Dyadobacter jejuensis sp. nov., isolated from seawater.Chun J, Kang JY, Joung Y, Kim H, Joh K, Jahng KYInt J Syst Evol Microbiol10.1099/ijs.0.043620-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Phosphatidylethanolamines/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny29737366Dyadobacter flavus sp. nov. and Dyadobacter terricola sp. nov., two novel members of the family Cytophagaceae isolated from forest soil.Dahal RH, Kim JArch Microbiol10.1007/s00203-018-1521-32018Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/*isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Forests, Phosphatidylethanolamines/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
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
21579Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100346Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100346)
30753Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172708428776041
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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/
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
88808Reimer, 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-ID403464.1