Strain identifier

BacDive ID: 10508

Type strain: Yes

Species: Vogesella perlucida

Strain Designation: DS-28

Strain history: <- LMG <- W.-M. Chen, Natl. Kaohsiung Marine Univ. Taiwan

NCBI tax ID(s): 450366 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 16504

BacDive-ID: 10508

DSM-Number: 22765

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

description: Vogesella perlucida DS-28 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from spring water.

NCBI tax id

  • NCBI tax id: 450366
  • Matching level: species

strain history

  • @ref: 16504
  • history: <- LMG <- W.-M. Chen, Natl. Kaohsiung Marine Univ. Taiwan

doi: 10.13145/bacdive10508.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Neisseriales
  • family: Chromobacteriaceae
  • genus: Vogesella
  • species: Vogesella perlucida
  • full scientific name: Vogesella perlucida Chou et al. 2008

@ref: 16504

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Neisseriales

family: Chromobacteriaceae

genus: Vogesella

species: Vogesella perlucida

full scientific name: Vogesella perlucida Chou et al. 2008

strain designation: DS-28

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32607negative01-02 µm0.5 µmrod-shapedyes
69480yes93.767
69480negative99.991

pigmentation

  • @ref: 32607
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16504
  • name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/535
  • composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16504positivegrowth28mesophilic
32607positivegrowth04-45
32607positiveoptimum30mesophilic

culture pH

@refabilitytypepHPH range
32607positivegrowth07-09alkaliphile
32607positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 32607
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32607no
69481no100
69480no99.992

halophily

@refsaltgrowthtested relationconcentration
32607NaClpositivegrowth0-2 %
32607NaClpositiveoptimum0.5 %

observation

  • @ref: 32607
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3260730089acetate+carbon source
3260722599arabinose+carbon source
3260722653asparagine+carbon source
3260717057cellobiose+carbon source
3260716947citrate+carbon source
3260715740formate+carbon source
3260728757fructose+carbon source
3260733984fucose+carbon source
3260728260galactose+carbon source
3260724265gluconate+carbon source
3260724996lactate+carbon source
3260729864mannitol+carbon source
3260737684mannose+carbon source
3260728053melibiose+carbon source
32607506227N-acetylglucosamine+carbon source
3260751850methyl pyruvate+carbon source
3260716634raffinose+carbon source
3260726546rhamnose+carbon source
3260730911sorbitol+carbon source
3260730031succinate+carbon source
3260717992sucrose+carbon source
3260727082trehalose+carbon source
3260717151xylitol+carbon source
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: yes

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
32607catalase+1.11.1.6
32607cytochrome oxidase+1.9.3.1
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
16504++------+--++----+--+
16504++------+--++----+--+

Isolation, sampling and environmental information

isolation

  • @ref: 16504
  • sample type: spring water
  • geographic location: southern Taiwan, Tainan County
  • country: Taiwan
  • origin.country: TWN
  • continent: Asia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Spring

taxonmaps

  • @ref: 69479
  • File name: preview.99_11242.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15355;96_559;97_1733;98_2118;99_11242&stattab=map
  • Last taxonomy: Vogesella
  • 16S sequence: EF626691
  • Sequence Identity:
  • Total samples: 3587
  • soil counts: 125
  • aquatic counts: 2157
  • animal counts: 1175
  • plant counts: 130

Safety information

risk assessment

  • @ref: 16504
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16504
  • description: Vogesella perlucida strain DS-28 16S ribosomal RNA gene, partial sequence
  • accession: EF626691
  • length: 1414
  • database: ena
  • NCBI tax ID: 450366

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vogesella perlucida DS-28GCA_007844155contigncbi450366
66792Vogesella perlucida strain DS-28450366.3wgspatric450366

GC content

  • @ref: 16504
  • GC-content: 61.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.723yes
anaerobicno96.408yes
halophileno94.431yes
spore-formingno93.969yes
glucose-utilyes91.502yes
aerobicyes79.389yes
flagellatedyes90.299no
thermophileno98.477no
motileyes92.216no
glucose-fermentno87.649yes

External links

@ref: 16504

culture collection no.: DSM 22765, BCRC 17730, LMG 24214

straininfo link

  • @ref: 79785
  • straininfo: 309046

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19060039Vogesella perlucida sp. nov., a non-pigmented bacterium isolated from spring water.Chou YJ, Chou JH, Lin MC, Arun AB, Young CC, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.65766-02008Fatty Acids/chemistry, Fresh Water/*microbiology, Genotype, Molecular Sequence Data, Neisseriaceae/*classification/genetics/isolation & purification/*physiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity, TaiwanGenetics
Phylogeny19625439Vogesella lacus sp. nov., isolated from a soft-shell turtle culture pond.Chou JH, Chou YJ, Arun AB, Young CC, Chen CA, Wang JT, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.009266-02009Animals, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Fresh Water/*microbiology, Molecular Sequence Data, Neisseriaceae/chemistry/classification/genetics/*isolation & purification, Phylogeny, RNA, Ribosomal, 16S/genetics, *TurtlesGenetics
Phylogeny19946047Vogesella mureinivorans sp. nov., a peptidoglycan-degrading bacterium from lake water.Jorgensen NOG, Brandt KK, Nybroe O, Hansen MInt J Syst Evol Microbiol10.1099/ijs.0.018630-02009Bacterial Typing Techniques, Base Composition, Chitinases/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Denmark, Fatty Acids/analysis, Fresh Water/*microbiology, Microscopy, Electron, Scanning, Microscopy, Electron, Transmission, Molecular Sequence Data, Muramidase/metabolism, Neisseriaceae/*classification/genetics/isolation & purification/*metabolism, Nucleic Acid Hybridization, Peptidoglycan/*metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAMetabolism
Phylogeny26198352Vogesella amnigena sp. nov., isolated from a freshwater river.Chen WM, Chen JC, Wang C, Huang CW, Sheu SYInt J Syst Evol Microbiol10.1099/ijsem.0.0004672015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydroxybutyrates/chemistry, Molecular Sequence Data, Neisseriaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Polyesters/chemistry, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Taiwan, Ubiquinone/chemistry, *Water MicrobiologyGenetics
Phylogeny26597454Description of Vogesella oryzae sp. nov., isolated from the rhizosphere of saline tolerant pokkali rice.Rameshkumar N, Lang E, Tanaka NSyst Appl Microbiol10.1016/j.syapm.2015.10.0032015Arabinose/metabolism, Bacterial Typing Techniques, Base Composition, Base Sequence, Chromobacterium/*classification/genetics/*isolation & purification, Citric Acid/metabolism, DNA Probes, DNA, Bacterial/genetics, Fatty Acids/analysis, Glucose/metabolism, India, Maltose/metabolism, Nucleic Acid Hybridization, Oryza/*microbiology, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Salt Tolerance, Sequence Analysis, DNA, Sodium Chloride, *Soil MicrobiologyMetabolism
Phylogeny31697226Vogesella urethralis sp. nov., isolated from human urine, and emended descriptions of Vogesella perlucida and Vogesella mureinivorans.Lan K, Cai YM, Li LH, Zeng JM, Yu XG, Qu PH, Li HL, Liu YY, Chen L, Chen C, Huang BInt J Syst Evol Microbiol10.1099/ijsem.0.0038022020Bacteria, Aerobic/genetics, Bacterial Typing Techniques, Base Composition, Betaproteobacteria/*classification/isolation & purification, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Humans, Hydroxybutyrates/metabolism, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Polyesters/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry, Urine/*microbiologyPathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16504Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22765)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22765
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
32607Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2882028776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68369Automatically annotated from API 20NE
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
79785Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309046.1StrainInfo: A central database for resolving microbial strain identifiers