Strain identifier

BacDive ID: 23879

Type strain: Yes

Species: Dyadobacter beijingensis

Strain Designation: A54

Strain history: CIP <- 2007, JCM <- 2006, Z. Dong, Capital Normal Univ., Beijing, China: strain A54

NCBI tax ID(s): 1121482 (strain), 365489 (species)

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General

@ref: 20531

BacDive-ID: 23879

DSM-Number: 21582

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

description: Dyadobacter beijingensis A54 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from rhizosphere of turf grasses irrigated with reclaimed water.

NCBI tax id

NCBI tax idMatching level
1121482strain
365489species

strain history

@refhistory
20531<- JCM <- Z. Dong; A54 <- X. Guo
116780CIP <- 2007, JCM <- 2006, Z. Dong, Capital Normal Univ., Beijing, China: strain A54

doi: 10.13145/bacdive23879.20230509.8.1

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 beijingensis
  • full scientific name: Dyadobacter beijingensis Dong et al. 2007

@ref: 20531

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Spirosomaceae

genus: Dyadobacter

species: Dyadobacter beijingensis

full scientific name: Dyadobacter beijingensis Dong et al. 2007 emend. Hahnke et al. 2016

strain designation: A54

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31981negativerod-shapedno
69480no91.285
69480negative99.995
116780negativerod-shapedno

pigmentation

  • @ref: 31981
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
20531NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37768MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116780CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
20531positivegrowth28mesophilic
31981positivegrowth04-35
31981positiveoptimum28mesophilic
37768positivegrowth30mesophilic

culture pH

@refabilitytypepH
31981positivegrowth06-08
31981positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31981aerobe
116780obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.965

halophily

@refsaltgrowthtested relationconcentration
31981NaClpositivegrowth0-1.5 %
31981NaClpositiveoptimum0.75 %

observation

  • @ref: 31981
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3198122599arabinose+carbon source
3198117057cellobiose+carbon source
3198116947citrate+carbon source
3198128757fructose+carbon source
3198133984fucose+carbon source
3198128260galactose+carbon source
3198117234glucose+carbon source
3198117716lactose+carbon source
3198117306maltose+carbon source
3198129864mannitol+carbon source
3198137684mannose+carbon source
3198128053melibiose+carbon source
3198117268myo-inositol+carbon source
3198116634raffinose+carbon source
3198117814salicin+carbon source
3198117992sucrose+carbon source
3198127082trehalose+carbon source
3198118222xylose+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose+builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch+builds acid from
6837116634raffinose+builds acid from
683716731melezitose+builds acid from
6837115443inulin+builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside+builds acid from
6837143943methyl alpha-D-mannoside+builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol+builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose+builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose+builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11678017632nitrate-reduction
11678016301nitrite-reduction

metabolite production

  • @ref: 116780
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31981catalase+1.11.1.6
31981cytochrome oxidase+1.9.3.1
116780oxidase+
116780catalase+1.11.1.6
116780urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase+3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116780-+++-++++-++++-++++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116780--++-+---++++-+-+--+++++++++++++++++--+++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
20531rhizosphere of turf grasses irrigated with reclaimed waterTaoranting Park, BeijingChinaCHNAsia
116780Rhizosphere, turf grassesBeijingChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_4902.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_496;96_2412;97_2936;98_3670;99_4902&stattab=map
  • Last taxonomy: Dyadobacter beijingensis
  • 16S sequence: DQ335125
  • Sequence Identity:
  • Total samples: 990
  • soil counts: 102
  • aquatic counts: 68
  • animal counts: 766
  • plant counts: 54

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
205311Risk group (German classification)
1167801Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31981
  • description: Dyadobacter beijingensis strain A54 16S ribosomal RNA gene, partial sequence
  • accession: DQ335125
  • length: 1411
  • database: nuccore
  • NCBI tax ID: 365489

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dyadobacter beijingensis DSM 21582GCA_000382205scaffoldncbi1121482
66792Dyadobacter beijingensis CGMCC 1.6375GCA_014645155scaffoldncbi365489
66792Dyadobacter beijingensis DSM 215821121482.3wgspatric1121482
66792Dyadobacter beijingensis strain CGMCC 1.6375365489.3wgspatric365489
66792Dyadobacter beijingensis DSM 215822522125168draftimg1121482

GC content

@refGC-contentmethod
3198149.2
2053152.1sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.513yes
flagellatedno97.557yes
gram-positiveno97.883yes
anaerobicno99.413yes
aerobicyes91.712no
halophileno95.559no
spore-formingno93.91no
thermophileno99.206no
glucose-utilyes89.371no
glucose-fermentno86.046no

External links

@ref: 20531

culture collection no.: DSM 21582, CGMCC 1.6375, JCM 14200, CIP 109570

straininfo link

  • @ref: 87890
  • straininfo: 302754

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17392220Dyadobacter beijingensis sp. nov., isolated from the rhizosphere of turf grasses in China.Dong Z, Guo X, Zhang X, Qiu F, Sun L, Gong H, Zhang FInt J Syst Evol Microbiol10.1099/ijs.0.64754-02007China, Cytophagaceae/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, Poaceae/*microbiology, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics
Phylogeny20008109Dyadobacter soli sp. nov., a starch-degrading bacterium isolated from farm soil.Lee M, Woo SG, Park J, Yoo SAInt J Syst Evol Microbiol10.1099/ijs.0.019653-02009Bacteroidetes/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Starch/*metabolismMetabolism
Phylogeny25604339Dyadobacter jiangsuensis sp. nov., a methyl red degrading bacterium isolated from a dye-manufacturing factory.Wang L, Chen L, Ling Q, Li CC, Tao Y, Wang MInt J Syst Evol Microbiol10.1099/ijs.0.0000692015Azo Compounds/*metabolism, Bacterial Typing Techniques, Base Composition, China, Coloring Agents/metabolism, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyMetabolism
Phylogeny27412002Dyadobacter endophyticus sp. nov., an endophytic bacterium isolated from maize root.Gao JL, Sun P, Wang XM, Qiu TL, Lv FY, Yuan M, Yang MM, Sun JGInt J Syst Evol Microbiol10.1099/ijsem.0.0013042016Bacterial Typing Techniques, Base Composition, Beijing, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Zea mays/*microbiologyTranscriptome

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
20531Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-21582Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21582)
31981Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172823528776041
37768Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7328
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
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
87890Reimer, 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-ID302754.1
116780Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109570Collection of Institut Pasteur (CIP 109570)