Strain identifier

BacDive ID: 164417

Type strain: Yes

Species: Dyadobacter luteus

Strain Designation: RS19

Strain history: L. Chen; Chin. Acad. of For., China; RS19.

NCBI tax ID(s): 2259619 (species)

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General

@ref: 67770

BacDive-ID: 164417

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

description: Dyadobacter luteus RS19 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from Rose rhizosphere soil in Mentougou District of Beijing.

NCBI tax id

  • NCBI tax id: 2259619
  • Matching level: species

strain history

  • @ref: 67770
  • history: L. Chen; Chin. Acad. of For., China; RS19.

doi: 10.13145/bacdive164417.20230509.8.1

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 luteus
  • full scientific name: Dyadobacter luteus Chen et al. 2020

@ref: 67770

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Spirosomaceae

genus: Dyadobacter

species: Dyadobacter luteus

full scientific name: Dyadobacter luteus Chen et al.

strain designation: RS19

type strain: yes

Morphology

cell morphology

  • @ref: 68257
  • gram stain: negative
  • cell length: 1.4-2.3 µm
  • cell width: 0.5-0.6 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 68257
  • colony size: 1-2 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 1 day
  • medium used: TSB agar

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
67770positivegrowth28mesophilic
68257positivegrowth1-37
68257positiveoptimum15-30

culture pH

  • @ref: 68257
  • ability: positive
  • type: growth
  • pH: 6-8

Physiology and metabolism

oxygen tolerance

  • @ref: 68257
  • oxygen tolerance: aerobe

halophily

  • @ref: 68257
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %(w/v)

observation

@refobservation
67770quinones: MK-7
68257occur in pairs in young cultures, but in chains of short rod shaped to coccoid cells in older cultures

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
682574853esculin+hydrolysis
682575291gelatin-hydrolysis
6825717632nitrate+reduction
6825717634D-glucose+assimilation
6825730849L-arabinose+assimilation
6825716024D-mannose+assimilation
68257506227N-acetyl-D-glucosamine+assimilation
6825717306maltose+assimilation
6825717306maltose+carbon source
6825716551D-trehalose+carbon source
6825717057cellobiose+carbon source
6825728066gentiobiose+carbon source
6825717992sucrose+carbon source
6825732528turanose+carbon source
6825717164stachyose+carbon source
6825716634raffinose+carbon source
6825736219alpha-lactose+carbon source
6825728053melibiose+carbon source
6825737657methyl D-glucoside+carbon source
6825717814D-salicin+carbon source
68257506227N-acetyl-D-glucosamine+carbon source
6825717925alpha-D-glucose+carbon source
6825716024D-mannose+carbon source
6825715824D-fructose+carbon source
6825712936D-galactose+carbon source
6825718287L-fucose+carbon source
6825762345L-rhamnose+carbon source
682571 % sodium lactate+carbon source
6825717309pectin+carbon source
6825718024D-galacturonic acid+carbon source
6825715895D-galactonic acid lactone+carbon source
6825728860beta-D-glucuronic acid+carbon source
6825717306maltose+energy source
6825716551D-trehalose+energy source
6825717057cellobiose+energy source
6825728066gentiobiose+energy source
6825717992sucrose+energy source
6825732528turanose+energy source
6825717164stachyose+energy source
6825716634raffinose+energy source
6825736219alpha-lactose+energy source
6825728053melibiose+energy source
6825737657methyl D-glucoside+energy source
6825717814D-salicin+energy source
68257506227N-acetyl-D-glucosamine+energy source
6825717925alpha-D-glucose+energy source
6825716024D-mannose+energy source
6825715824D-fructose+energy source
6825712936D-galactose+energy source
6825718287L-fucose+energy source
6825762345L-rhamnose+energy source
682571 % sodium lactate+energy source
6825717309pectin+energy source
6825718024D-galacturonic acid+energy source
6825715895D-galactonic acid lactone+energy source
6825728860beta-D-glucuronic acid+energy source

enzymes

@refvalueactivityec
68257catalase+1.11.1.6
68257cytochrome oxidase+1.9.3.1
68257alkaline phosphatase+3.1.3.1
68257esterase (C 4)+
68257esterase Lipase (C 8)+
68257leucine arylamidase+3.4.11.1
68257valine arylamidase+
68257cystine arylamidase+3.4.11.3
68257acid phosphatase+3.1.3.2
68257esterase+
68257naphthol-AS-BI-phosphohydrolase+
68257alpha-galactosidase+3.2.1.22
68257beta-galactosidase+3.2.1.23
68257alpha-glucosidase+3.2.1.20
68257beta-glucosidase+3.2.1.21
68257N-acetyl-beta-glucosaminidase+3.2.1.52
68257alpha-mannosidase+3.2.1.24
68257lipase (C 14)-
68257trypsin-3.4.21.4
68257chymotrypsin-3.4.4.5
68257beta-glucuronidase-3.2.1.31
68257beta-D-fucosidase-3.2.1.38
68257P-nitroso-D-methyl galactose-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    68257C15:1 iso G5
    68257C15:0 iso18.5
    68257C15:0 anteiso1.5
    68257C16:1 w5c14.5
    68257C16:04.5
    68257C15:0 iso 3OH5.7
    68257C17:0 iso 3OH9.2
    68257C16:1 w6c/C16:1 w7c36.1
  • type of FA analysis: whole cell analysis
  • incubation medium: TSA
  • incubation temperature: 28
  • incubation time: 2.5
  • software version: Sherlock 6.0
  • system: MIS MIDI
  • instrument: 6890N gas chromatograph
  • method/protocol: Sasser, 2001

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationlatitudelongitudeenrichment cultureisolation date
67770Rose rhizosphere soil in Mentougou District of BeijingChinaCHNAsia
68257soil of rose rhizosphereChinaCHNAsiaMentougou District of Beijing39.9633116.083LB2016-05-01

Sequence information

16S sequences

  • @ref: 68257
  • description: Dyadobacter luteus 16S ribosomal RNA gene, partial sequence
  • accession: MH558673
  • length: 1398
  • database: ena
  • NCBI tax ID: 2259619

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dyadobacter luteus RS192839216549draftimg2259619
67770Dyadobacter luteus RS19GCA_003383615contigncbi2259619

GC content

  • @ref: 67770
  • GC-content: 43.1
  • method: genome sequence analysis

External links

@ref: 67770

culture collection no.: JCM 32940, ACCC 60381, CGMCC 1.13719

literature

  • topic: Phylogeny
  • Pubmed-ID: 31595323
  • title: Dyadobacter luteus sp. nov., isolated from rose rhizosphere soil.
  • authors: Chen L, Gao X, Ma Q, Liu H, Wang X, Xu Y, Liu Y
  • journal: Arch Microbiol
  • DOI: 10.1007/s00203-019-01738-5
  • year: 2019
  • mesh: Bacterial Typing Techniques, Base Composition, Cytophagaceae/chemistry/*classification/genetics, DNA, Bacterial/genetics, Fatty Acids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Rosa/microbiology, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Vitamin K 2/analysis
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournal
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
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/
68257Lin Chen, Xu Gao, Qinghua Ma, Huihui Liu, Xinghong Wang, Yan Xu and Yunpeng LiuDyadobacter luteus sp. nov., isolated from rose rhizosphere soil10.1007/s00203-019-01738-5Arch Microbiol 202: 191-196 2020