Strain identifier

BacDive ID: 141034

Type strain: Yes

Species: Dyella caseinilytica

Strain Designation: DHOB09

NCBI tax ID(s): 1849581 (species)

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General

@ref: 43916

BacDive-ID: 141034

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

description: Dyella caseinilytica DHOB09 is an aerobe, Gram-negative, rod-shaped bacterium that forms irregular colonies and was isolated from upper layer of forest soil of Dinghushan Biosphere Reserve, Guangdong Province, PR China.

NCBI tax id

  • NCBI tax id: 1849581
  • Matching level: species

doi: 10.13145/bacdive141034.20230509.8.1

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 caseinilytica
  • full scientific name: Dyella caseinilytica Xia et al. 2017

@ref: 43916

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Lysobacterales

family: Rhodanobacteraceae

genus: Dyella

species: Dyella caseinilytica

strain designation: DHOB09

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43916negative1.3-1.9 µm0.3-0.5 µmrod-shapedno
69480yes96.275
69480negative99.974

colony morphology

  • @ref: 43916
  • colony size: 0.7-1.2 mm
  • colony color: dark yellow
  • colony shape: irregular
  • incubation period: 4 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

@refnamegrowth
43916LB (Luria-Bertani) MEDIUMno
43916MacConkey agarno
43916Nutrient agar (NA)yes
43916Reasoner's 2A agar (R2A)yes
43916Tryptic soy agaryes

culture temp

@refgrowthtypetemperaturerange
43916positivegrowth10-42
43916positiveoptimum25-28mesophilic

culture pH

@refabilitytypepHPH range
43916positivegrowth5.5-9.0alkaliphile
43916positiveoptimum7.0-7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 43916
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
43916no
69481no100
69480no99.989

halophily

@refsaltgrowthtested relationconcentration
43916NaClpositivegrowth0-4 %(w/v)
43916NaClpositiveoptimum0-0.5 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43916168082-dehydro-D-gluconate-carbon source
43916581435-dehydro-D-gluconate-carbon source
4391617128adipate-carbon source
4391627689decanoate-carbon source
4391617057cellobiose-carbon source
4391615963ribitol-carbon source
4391617108D-arabinose-carbon source
4391618333D-arabitol-carbon source
4391628847D-fucose-carbon source
4391662318D-lyxose-carbon source
4391616899D-mannitol-carbon source
4391616988D-ribose-carbon source
4391617924D-sorbitol-carbon source
4391616443D-tagatose-carbon source
4391616813galactitol-carbon source
4391617113erythritol-carbon source
4391628066gentiobiose-carbon source
4391615978glycerol 3-phosphate-carbon source
4391628087glycogen-carbon source
4391617268myo-inositol-carbon source
4391630849L-arabinose-carbon source
4391618403L-arabitol-carbon source
4391618287L-fucose-carbon source
4391662345L-rhamnose-carbon source
4391617266L-sorbose-carbon source
4391665328L-xylose-carbon source
4391617716lactose-carbon source
4391625115malate-carbon source
439166731melezitose-carbon source
43916320061methyl alpha-D-glucopyranoside-carbon source
4391674863methyl beta-D-xylopyranoside-carbon source
4391618401phenylacetate-carbon source
4391632032potassium gluconate-carbon source
4391616634raffinose-carbon source
4391617814salicin-carbon source
4391653258sodium citrate-carbon source
4391628017starch-carbon source
4391617992sucrose-carbon source
4391632528turanose-carbon source
4391617151xylitol-carbon source
4391629016arginine-hydrolysis
4391616991dna-hydrolysis
439164853esculin-hydrolysis
4391653426tween 80-hydrolysis
4391615824D-fructose+carbon source
4391612936D-galactose+carbon source
4391617634D-glucose+carbon source
4391616024D-mannose+carbon source
4391665327D-xylose+carbon source
43916esculin ferric citrate+carbon source
4391615443inulin+carbon source
43916maltose hydrate+carbon source
4391628053melibiose+carbon source
43916506227N-acetylglucosamine+carbon source
4391627082trehalose+carbon source
43916casein+hydrolysis
439165291gelatin+hydrolysis
4391628017starch+hydrolysis
4391653424tween 20+hydrolysis
4391617632nitrate+reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
43916100241ciprofloxacinyesyes5 µg (disc)
4391617833gentamicinyesyes10 µg (disc)
439166104kanamycinyesyes30 µg (disc)
4391628368novobiocinyesyes5 µg (disc)
4391659062polymyxinyesyes300 Unit (disc)
4391617076streptomycinyesyes10 µg (disc)
4391628864tobramycinyesyes10 µg (disc)
4391628001vancomycinyesyes30 µg (disc)
4391618208penicillin gyesyes10 Unit (disc)
4391617698chloramphenicolyesyes30 µg (disc)
4391648923erythromycinyesyes15 µg (disc)
4391627902tetracyclineyesyes30 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
4391616136hydrogen sulfideno
4391635581indoleno

enzymes

@refvalueactivityec
43916cytochrome oxidase+1.9.3.1
43916catalase+1.11.1.6
43916alkaline phosphatase+3.1.3.1
43916esterase (C 4)+
43916esterase Lipase (C 8)+
43916leucine arylamidase+3.4.11.1
43916valine arylamidase+
43916cystine arylamidase+3.4.11.3
43916acid phosphatase+3.1.3.2
43916alpha-galactosidase+3.2.1.22
43916beta-galactosidase+3.2.1.23
43916naphthol-AS-BI-phosphohydrolase+
43916alpha-glucosidase+3.2.1.20
43916beta-glucosidase+3.2.1.21
43916alpha-mannosidase+3.2.1.24
43916N-acetyl-beta-glucosaminidase+3.2.1.52
43916alpha-fucosidase+3.2.1.51
43916urease+3.5.1.5
43916lipase (C 14)-
43916trypsin-3.4.21.4
43916alpha-chymotrypsin-3.4.21.1
43916beta-glucuronidase-3.2.1.31

Isolation, sampling and environmental information

isolation

  • @ref: 43916
  • sample type: upper layer of forest soil of Dinghushan Biosphere Reserve, Guangdong Province, PR China
  • geographic location: Dinghushan Biosphere Reserve, Guangdong Province
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 23.1667
  • longitude: 112.517
  • enrichment culture: MM1F medium
  • enrichment culture composition: 0.04 g/L MgSO4.7H2O, 0.02 g/L CaCl2.2H2O, 0.05 g/L yeast extract, 0.5 g/L fructose, 15 g/L agar, pH 5.0

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dyella caseinilytica DHOB09GCA_016865235completencbi1849581
66792Dyella caseinilytica CGMCC 1.15434GCA_014642815contigncbi1849581
66792Dyella caseinilytica strain CGMCC 1.154341849581.3wgspatric1849581

GC content

  • @ref: 43916
  • GC-content: 59.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno78.719no
gram-positiveno98.205no
anaerobicno99.296yes
aerobicyes92no
halophileno94.532no
spore-formingno95.037no
thermophileno99.007yes
glucose-utilyes92.883yes
motileyes75.277yes
glucose-fermentno84.936no

External links

@ref: 43916

culture collection no.: CGMCC 1.15434, LMG 29202

literature

  • topic: Phylogeny
  • Pubmed-ID: 28840798
  • title: Dyella caseinilytica sp. nov., Dyella flava sp. nov. and Dyella mobilis sp. nov., isolated from forest soil.
  • authors: Xia F, Chen MH, Lv YY, Zhang HY, Qiu LH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002090
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry, Xanthomonadaceae/*classification/genetics/isolation & purification
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
43916Fan Xia, Mei-hong Chen, Ying-ying Lv, Han-yun Zhang, Li-hong QiuDyella caseinilytica sp. nov., Dyella flava sp. nov. and Dyella mobilis sp. nov., isolated from forest soil10.1099/ijsem.0.002090IJSEM 67: 3237-3245 201728840798
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
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