Strain identifier
BacDive ID: 10508
Type strain:
Species: Vogesella perlucida
Strain Designation: DS-28
Strain history: <- LMG <- W.-M. Chen, Natl. Kaohsiung Marine Univ. Taiwan
NCBI tax ID(s): 450366 (species)
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
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
32607 | negative | 01-02 µm | 0.5 µm | rod-shaped | yes | |
69480 | yes | 93.767 | ||||
69480 | negative | 99.991 |
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
16504 | positive | growth | 28 | mesophilic |
32607 | positive | growth | 04-45 | |
32607 | positive | optimum | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
32607 | positive | growth | 07-09 | alkaliphile |
32607 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 32607
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
32607 | no | |
69481 | no | 100 |
69480 | no | 99.992 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
32607 | NaCl | positive | growth | 0-2 % |
32607 | NaCl | positive | optimum | 0.5 % |
observation
- @ref: 32607
- observation: aggregates in chains
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32607 | 30089 | acetate | + | carbon source |
32607 | 22599 | arabinose | + | carbon source |
32607 | 22653 | asparagine | + | carbon source |
32607 | 17057 | cellobiose | + | carbon source |
32607 | 16947 | citrate | + | carbon source |
32607 | 15740 | formate | + | carbon source |
32607 | 28757 | fructose | + | carbon source |
32607 | 33984 | fucose | + | carbon source |
32607 | 28260 | galactose | + | carbon source |
32607 | 24265 | gluconate | + | carbon source |
32607 | 24996 | lactate | + | carbon source |
32607 | 29864 | mannitol | + | carbon source |
32607 | 37684 | mannose | + | carbon source |
32607 | 28053 | melibiose | + | carbon source |
32607 | 506227 | N-acetylglucosamine | + | carbon source |
32607 | 51850 | methyl pyruvate | + | carbon source |
32607 | 16634 | raffinose | + | carbon source |
32607 | 26546 | rhamnose | + | carbon source |
32607 | 30911 | sorbitol | + | carbon source |
32607 | 30031 | succinate | + | carbon source |
32607 | 17992 | sucrose | + | carbon source |
32607 | 27082 | trehalose | + | carbon source |
32607 | 17151 | xylitol | + | carbon source |
68369 | 25115 | malate | + | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | - | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | + | assimilation |
68369 | 16899 | D-mannitol | + | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | + | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | - | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | + | energy source |
68369 | 17632 | nitrate | + | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: yes
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: +
enzymes
@ref | value | activity | ec |
---|---|---|---|
32607 | catalase | + | 1.11.1.6 |
32607 | cytochrome oxidase | + | 1.9.3.1 |
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | - | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Vogesella perlucida DS-28 | GCA_007844155 | contig | ncbi | 450366 |
66792 | Vogesella perlucida strain DS-28 | 450366.3 | wgs | patric | 450366 |
GC content
- @ref: 16504
- GC-content: 61.8
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 98.723 | yes |
anaerobic | no | 96.408 | yes |
halophile | no | 94.431 | yes |
spore-forming | no | 93.969 | yes |
glucose-util | yes | 91.502 | yes |
aerobic | yes | 79.389 | yes |
flagellated | yes | 90.299 | no |
thermophile | no | 98.477 | no |
motile | yes | 92.216 | no |
glucose-ferment | no | 87.649 | yes |
External links
@ref: 16504
culture collection no.: DSM 22765, BCRC 17730, LMG 24214
straininfo link
- @ref: 79785
- straininfo: 309046
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19060039 | Vogesella perlucida sp. nov., a non-pigmented bacterium isolated from spring water. | Chou YJ, Chou JH, Lin MC, Arun AB, Young CC, Chen WM | Int J Syst Evol Microbiol | 10.1099/ijs.0.65766-0 | 2008 | Fatty Acids/chemistry, Fresh Water/*microbiology, Genotype, Molecular Sequence Data, Neisseriaceae/*classification/genetics/isolation & purification/*physiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity, Taiwan | Genetics |
Phylogeny | 19625439 | Vogesella lacus sp. nov., isolated from a soft-shell turtle culture pond. | Chou JH, Chou YJ, Arun AB, Young CC, Chen CA, Wang JT, Chen WM | Int J Syst Evol Microbiol | 10.1099/ijs.0.009266-0 | 2009 | Animals, 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, *Turtles | Genetics |
Phylogeny | 19946047 | Vogesella mureinivorans sp. nov., a peptidoglycan-degrading bacterium from lake water. | Jorgensen NOG, Brandt KK, Nybroe O, Hansen M | Int J Syst Evol Microbiol | 10.1099/ijs.0.018630-0 | 2009 | Bacterial 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, DNA | Metabolism |
Phylogeny | 26198352 | Vogesella amnigena sp. nov., isolated from a freshwater river. | Chen WM, Chen JC, Wang C, Huang CW, Sheu SY | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000467 | 2015 | Bacterial 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 Microbiology | Genetics |
Phylogeny | 26597454 | Description of Vogesella oryzae sp. nov., isolated from the rhizosphere of saline tolerant pokkali rice. | Rameshkumar N, Lang E, Tanaka N | Syst Appl Microbiol | 10.1016/j.syapm.2015.10.003 | 2015 | Arabinose/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 Microbiology | Metabolism |
Phylogeny | 31697226 | Vogesella 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 B | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003802 | 2020 | Bacteria, 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/*microbiology | Pathogenicity |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
16504 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22765) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22765 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
32607 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28820 | 28776041 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
68369 | Automatically annotated from API 20NE | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
79785 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID309046.1 | StrainInfo: A central database for resolving microbial strain identifiers |