Strain identifier

BacDive ID: 17453

Type strain: Yes

Species: Dyella japonica

Strain Designation: XD53

Strain history: IAM 15069 <-- C.-H. Xie XD53.

NCBI tax ID(s): 1440762 (strain), 231455 (species)

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General

@ref: 6351

BacDive-ID: 17453

DSM-Number: 16301

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

description: Dyella japonica XD53 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1440762strain
231455species

strain history

@refhistory
6351<- C.-H. Xie and A. Yokota; XD53
67770IAM 15069 <-- C.-H. Xie XD53.

doi: 10.13145/bacdive17453.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Rhodanobacteraceae
  • genus: Dyella
  • species: Dyella japonica
  • full scientific name: Dyella japonica Xie and Yokota 2005

@ref: 6351

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Rhodanobacteraceae

genus: Dyella

species: Dyella japonica

full scientific name: Dyella japonica Xie and Yokota 2005

strain designation: XD53

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31351negative1.2 µm0.4 µmrod-shapedyes
69480yes95.716
69480negative99.992

pigmentation

  • @ref: 31351
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 6351
  • 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) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
6351positivegrowth30mesophilic
31351positivegrowth10-37
31351positiveoptimum27.5mesophilic
61583positivegrowth30mesophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepH
31351positivegrowth5.6-8.0
31351positiveoptimum6.85

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31351aerobe
61583aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.956

observation

@refobservation
31351aggregates in clumps
67770quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3135128757fructose+carbon source
3135117234glucose+carbon source
3135125017leucine+carbon source
3135117306maltose+carbon source
3135137684mannose+carbon source
31351506227N-acetylglucosamine+carbon source
3135117632nitrate+reduction

enzymes

@refvalueactivityec
31351acid phosphatase+3.1.3.2
31351alkaline phosphatase+3.1.3.1
31351catalase+1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6351soilTokyoJapanJPNAsia
61583SoilTokyoJapanJPNAsia
67770SoilTokyoJapanJPNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_5541.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_114;96_316;97_3161;98_3972;99_5541&stattab=map
  • Last taxonomy: Dyella
  • 16S sequence: AB110498
  • Sequence Identity:
  • Total samples: 2961
  • soil counts: 2327
  • aquatic counts: 143
  • animal counts: 282
  • plant counts: 209

Safety information

risk assessment

  • @ref: 6351
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6351
  • description: Dyella japonica gene for 16S ribosomal RNA, partial sequence, strain:XD53
  • accession: AB110498
  • length: 1485
  • database: ena
  • NCBI tax ID: 231455

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dyella japonica DSM 163011440762.4wgspatric1440762
66792Dyella japonica DSM 163012639762820draftimg1440762
67770Dyella japonica DSM 16301GCA_001010355contigncbi1440762

GC content

@refGC-contentmethod
635163.5
3135163.7
6777063.5high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes87.974yes
gram-positiveno97.56yes
anaerobicno98.451yes
halophileno95.642no
spore-formingno94.693no
thermophileno98.772no
glucose-utilyes88.16yes
aerobicyes87.287yes
flagellatedno82.659no
glucose-fermentno85.985no

External links

@ref: 6351

culture collection no.: DSM 16301, ATCC BAA 939, IAM 15069, CCUG 58062, JCM 21530, NBRC 102414

straininfo link

  • @ref: 86449
  • straininfo: 138000

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15774657Dyella japonica gen. nov., sp. nov., a gamma-proteobacterium isolated from soil.Xie CH, Yokota AInt J Syst Evol Microbiol10.1099/ijs.0.63377-02005Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Gammaproteobacteria/*classification/genetics/isolation & purification/physiology, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Xanthomonadaceae/*classification/genetics/isolation & purification/physiologyEnzymology
Phylogeny16902003Rhodanobacter spathiphylli sp. nov., a gammaproteobacterium isolated from the roots of Spathiphyllum plants grown in a compost-amended potting mix.De Clercq D, Van Trappen S, Cleenwerck I, Ceustermans A, Swings J, Coosemans J, Ryckeboer JInt J Syst Evol Microbiol10.1099/ijs.0.64131-02006Antibiosis, Araceae/growth & development/*microbiology, Base Composition, Catalase/analysis, Culture Media, DNA, Bacterial, Fatty Acids/analysis, Gammaproteobacteria/chemistry/*classification/isolation & purification/physiology, Hypocreales/physiology, Molecular Sequence Data, Oxidoreductases/analysis, Phylogeny, Plant Diseases/microbiology, Plant Roots/microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Soil, Soil Microbiology, Species SpecificityCultivation
Phylogeny19244422Dyella ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea.Jung HM, Ten LN, Kim KH, An DS, Im WT, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.64514-02009Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, *Panax/growth & development, Phenotype, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Xanthomonadaceae/*classification/genetics/isolation & purification/physiologyGenetics
Phylogeny21296929Rhodanobacter panaciterrae sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a ginseng field.Wang L, An DS, Kim SG, Jin FX, Lee ST, Im WTInt J Syst Evol Microbiol10.1099/ijs.0.025718-02011DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Ginsenosides/*metabolism, Molecular Sequence Data, Panax/growth & development/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Xanthomonadaceae/*classification/genetics/*isolation & purification/metabolismMetabolism
Phylogeny30608226Dyella solisilvae sp. nov., isolated from mixed pine and broad-leaved forest soil.Gao ZH, Yang Z, Chen MH, Huang ZJ, Qiu LHInt J Syst Evol Microbiol10.1099/ijsem.0.0032182019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, Pinus, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry, Xanthomonadaceae/*classification/isolation & purificationTranscriptome
Phylogeny31454308Dyella amyloliquefaciens sp. nov., isolated from forest soil.Fu JC, Gao ZH, Wu TT, Chen MH, Qiu LHInt J Syst Evol Microbiol10.1099/ijsem.0.0036602019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, Phospholipids/chemistry, Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry, Xanthomonadaceae/*classification/isolation & purificationTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6351Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16301)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16301
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
31351Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2766428776041
61583Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 58062)https://www.ccug.se/strain?id=58062
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
86449Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138000.1StrainInfo: A central database for resolving microbial strain identifiers