Strain identifier

BacDive ID: 23880

Type strain: Yes

Species: Dyadobacter soli

Strain Designation: MJ20

Strain history: <- MJ Lee, H-Plus Eco, Korea [6658]

NCBI tax ID(s): 659014 (species)

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General

@ref: 20532

BacDive-ID: 23880

DSM-Number: 25329

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

description: Dyadobacter soli MJ20 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from farm soil.

NCBI tax id

  • NCBI tax id: 659014
  • Matching level: species

strain history

@refhistory
20532<- JCM <- M.-J. Lee, KRIBB
67770M. J. Lee MJ20.
67771<- MJ Lee, H-Plus Eco, Korea [6658]

doi: 10.13145/bacdive23880.20230509.8.1

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 soli
  • full scientific name: Dyadobacter soli Lee et al. 2010

@ref: 20532

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Spirosomaceae

genus: Dyadobacter

species: Dyadobacter soli

full scientific name: Dyadobacter soli Lee et al. 2010

strain designation: MJ20

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29732negative1.9-2.4 µm0.6-0.7 µmrod-shapedno
67771rod-shapedno
67771negative
69480no90.419
69480negative99.988

pigmentation

  • @ref: 29732
  • production: yes

multimedia

  • @ref: 20532
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_25329.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 20532
  • 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
20532positivegrowth28mesophilic
29732positivegrowth15-30
29732positiveoptimum25mesophilic
67770positivegrowth25mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepH
29732positivegrowth05-08
29732positiveoptimum6.5-7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29732aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.97

observation

@refobservation
29732aggregates in chains
67770quinones: MK-7
67771quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
29732168082-dehydro-D-gluconate+carbon source
2973222599arabinose+carbon source
2973217234glucose+carbon source
2973225115malate+carbon source
2973217306maltose+carbon source
2973237684mannose+carbon source
2973228053melibiose+carbon source
29732506227N-acetylglucosamine+carbon source
2973218401phenylacetate+carbon source
2973226546rhamnose+carbon source
2973217992sucrose+carbon source

enzymes

@refvalueactivityec
29732catalase+1.11.1.6
29732cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
20532farm soilnear DaejeonRepublic of KoreaKORAsia
67770Farm soil near DaejeonRepublic of KoreaKORAsia
67771From soilRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Field
#Engineered#Food production#Aquaculture

taxonmaps

  • @ref: 69479
  • File name: preview.99_5763.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_496;96_2412;97_2936;98_3670;99_5763&stattab=map
  • Last taxonomy: Dyadobacter
  • 16S sequence: GQ241324
  • Sequence Identity:
  • Total samples: 3843
  • soil counts: 517
  • aquatic counts: 233
  • animal counts: 2781
  • plant counts: 312

Safety information

risk assessment

  • @ref: 20532
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20532
  • description: Dyadobacter soli strain MJ20 16S ribosomal RNA gene, partial sequence
  • accession: GQ241324
  • length: 1398
  • database: ena
  • NCBI tax ID: 659014

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dyadobacter soli strain DSM 25329659014.3wgspatric659014
66792Dyadobacter soli DSM 253292619619010draftimg659014
67770Dyadobacter soli DSM 25329GCA_900101885scaffoldncbi659014

GC content

@refGC-contentmethod
2053248.5high performance liquid chromatography (HPLC)
2973248.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.02yes
anaerobicno99.333yes
halophileno95.255no
spore-formingno92.101no
glucose-utilyes87.248no
thermophileno99.033yes
flagellatedno97.229yes
motileno91.779no
aerobicyes89.524yes
glucose-fermentno86.819no

External links

@ref: 20532

culture collection no.: DSM 25329, JCM 16232, KCTC 22481

straininfo link

  • @ref: 87891
  • straininfo: 404040

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Phylogeny30566070Dyadobacter luticola sp. nov., isolated from a sewage sediment sample.Song Z, Song Y, Yu Y, Choi L, Wang G, Li MInt J Syst Evol Microbiol10.1099/ijsem.0.0031782018Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

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
20532Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-25329Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25329)
29732Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172611428776041
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
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.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
87891Reimer, 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-ID404040.1