Strain identifier

BacDive ID: 132636

Type strain: Yes

Species: Dyadobacter endophyticus

Strain Designation: 65

Strain history: <- J.-l. Gao, Beijing Academy of Agriculture and Forestry Science; 65 <-

NCBI tax ID(s): 1749036 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 24425

BacDive-ID: 132636

DSM-Number: 100786

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

description: Dyadobacter endophyticus 65 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from surface-sterilized root tissue of maize.

NCBI tax id

  • NCBI tax id: 1749036
  • Matching level: species

strain history

  • @ref: 24425
  • history: <- J.-l. Gao, Beijing Academy of Agriculture and Forestry Science; 65 <-

doi: 10.13145/bacdive132636.20230509.8.1

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 endophyticus
  • full scientific name: Dyadobacter endophyticus Gao et al. 2016

@ref: 24425

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Spirosomaceae

genus: Dyadobacter

species: Dyadobacter endophyticus

full scientific name: Dyadobacter endophyticus Gao et al. 2016

strain designation: 65

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
24908negative0.6-1.5 µm0.4-0.6 µmrod-shaped
69480no93.253
69480negative99.997

colony morphology

  • @ref: 24908
  • colony size: 1.0-1.5 mm
  • colony color: yellowish
  • colony shape: circular
  • incubation period: 4 days
  • medium used: LB agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24908LB (Luria-Bertani) MEDIUMyes
24425NUTRIENT 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

culture temp

@refgrowthtypetemperaturerange
24908positivegrowth20-45
24908positiveoptimum30mesophilic
24425positivegrowth28mesophilic

culture pH

@refabilitytypepH
24908positivegrowth6.0-8.0
24908positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 24908
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.994

halophily

  • @ref: 24908
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2490827613amygdalin+builds acid from
2490818305arbutin+builds acid from
2490817057cellobiose+builds acid from
2490815824D-fructose+builds acid from
2490817634D-glucose+builds acid from
2490817716lactose+builds acid from
2490816024D-mannose+builds acid from
2490865327D-xylose+builds acid from
249084853esculin+builds acid from
2490828066gentiobiose+builds acid from
2490815443inulin+builds acid from
2490817306maltose+builds acid from
249086731melezitose+builds acid from
2490828053melibiose+builds acid from
24908320061methyl alpha-D-glucopyranoside+builds acid from
24908506227N-acetylglucosamine+builds acid from
2490816634raffinose+builds acid from
2490817814salicin+builds acid from
2490817992sucrose+builds acid from
2490827082trehalose+builds acid from
2490832528turanose+builds acid from
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
24908acid phosphatase+3.1.3.2
24908alkaline phosphatase+3.1.3.1
24908alpha-chymotrypsin-3.4.21.1
24908alpha-fucosidase-3.2.1.51
24908alpha-galactosidase+3.2.1.22
24908alpha-glucosidase+3.2.1.20
24908alpha-mannosidase+3.2.1.24
24908beta-galactosidase+3.2.1.23
24908beta-glucosidase+3.2.1.21
24908beta-glucuronidase-3.2.1.31
24908catalase+1.11.1.6
24908cystine arylamidase+3.4.11.3
24908cytochrome oxidase+1.9.3.1
24908esterase (C 4)+
24908esterase lipase (C 8)+
24908leucine arylamidase+3.4.11.1
24908lipase (C 14)-
24908N-acetyl-beta-glucosaminidase+3.2.1.52
24908naphthol-AS-BI-phosphohydrolase+
24908trypsin+3.4.21.4
24908valine arylamidase+
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
24425-----+-++++-++------+

Isolation, sampling and environmental information

isolation

  • @ref: 24425
  • sample type: surface-sterilized root tissue of maize
  • geographic location: Beijing, Fangshan District
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)
#Host Body-Site#Plant#Sterilized plant part

Safety information

risk assessment

  • @ref: 24425
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24425
  • description: Dyadobacter endophyticus strain 65 16S ribosomal RNA gene, partial sequence
  • accession: KT003984
  • length: 1374
  • database: ena
  • NCBI tax ID: 1749036

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dyadobacter endophyticus CGMCC 1.15288GCA_014641595scaffoldncbi1749036
66792Dyadobacter endophyticus strain CGMCC 1.152881749036.3wgspatric1749036

GC content

@refGC-contentmethod
2490846.6Thermal denaturation, fluorometry
2442546.6thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno96.964no
gram-positiveno98.017yes
anaerobicno99.485yes
aerobicyes88.709yes
halophileno95.808yes
spore-formingno91.942no
thermophileno99.575yes
glucose-utilyes87.394no
motileno92.31no
glucose-fermentno87.937yes

External links

@ref: 24425

culture collection no.: DSM 100786, CGMCC 1.15288

straininfo link

  • @ref: 90950
  • straininfo: 402180

literature

  • topic: Phylogeny
  • Pubmed-ID: 27412002
  • title: Dyadobacter endophyticus sp. nov., an endophytic bacterium isolated from maize root.
  • authors: Gao JL, Sun P, Wang XM, Qiu TL, Lv FY, Yuan M, Yang MM, Sun JG
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001304
  • year: 2016
  • mesh: Bacterial 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/*microbiology
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24425Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100786Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100786)
24908J.-l. S. Gao, Pengbo,Wang, Xu-ming,Qiu, Tian-lei,Lv, Fan-yang,Yuan, Mei,Yang, Ming-ming,Sun, Jian-guangDyadobacter endophyticus sp. nov., an endophytic bacterium isolated from maize root10.1099/ijsem.0.001304IJSEM 66: 4022-4026 201627412002
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
68369Automatically annotated from API 20NE
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
90950Reimer, 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-ID402180.1