Strain identifier
BacDive ID: 131263
Type strain: 
Species: Vogesella fluminis
Strain Designation: Npb-07
Strain history: <- LMG <- W.-M. Chen, National Kaohsiung Marine University, Taiwan; Npb-07
NCBI tax ID(s): 1069161 (species)
version 8.1 (current version)
General
@ref: 22490
BacDive-ID: 131263
DSM-Number: 100851
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Vogesella fluminis Npb-07 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from freshwater river.
NCBI tax id
- NCBI tax id: 1069161
- Matching level: species
strain history
- @ref: 22490
- history: <- LMG <- W.-M. Chen, National Kaohsiung Marine University, Taiwan; Npb-07
doi: 10.13145/bacdive131263.20230509.8.1
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 fluminis
- full scientific name: Vogesella fluminis Sheu et al. 2013
@ref: 22490
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Chromobacteriaceae, not assigned to order
family: Chromobacteriaceae
genus: Vogesella
species: Vogesella fluminis
full scientific name: Vogesella fluminis Sheu et al. 2013
strain designation: Npb-07
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 30966 | negative | 1.15 µm | 0.4 µm | rod-shaped | yes | |
| 69480 | yes | 92.821 | ||||
| 69480 | negative | 99.998 |
pigmentation
- @ref: 30966
- production: yes
Culture and growth conditions
culture medium
- @ref: 22490
- name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830c
- composition: Name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 22490 | positive | growth | 28 | mesophilic |
| 30966 | positive | growth | 10-37 | |
| 30966 | positive | optimum | 25 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 30966 | positive | growth | 6.0-9.0 | alkaliphile |
| 30966 | positive | optimum | 6.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 30966
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 30966 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.999 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 30966 | NaCl | positive | growth | 0-1 % |
| 30966 | NaCl | positive | optimum | 0.5 % |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30966 | 17234 | glucose | + | carbon source |
| 30966 | 29987 | glutamate | + | carbon source |
| 30966 | 26271 | proline | + | carbon source |
| 30966 | 53423 | tween 40 | + | carbon source |
| 30966 | 53426 | tween 80 | + | carbon source |
| 30966 | 17632 | nitrate | + | reduction |
| 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 |
|---|---|---|---|
| 30966 | acid phosphatase | + | 3.1.3.2 |
| 30966 | catalase | + | 1.11.1.6 |
| 30966 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 22490 | + | + | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | + | - | - | + |
Isolation, sampling and environmental information
isolation
- @ref: 22490
- sample type: freshwater river
- geographic location: near Pingtung, Beishi River
- country: Taiwan
- origin.country: TWN
- continent: Asia
- latitude: 22.3703
- longitude: 120.592
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Freshwater |
| #Environmental | #Aquatic | #River (Creek) |
Safety information
risk assessment
- @ref: 22490
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22490
- description: Vogesella fluminis strain Npb-07 16S ribosomal RNA gene, partial sequence
- accession: JN315669
- length: 1409
- database: ena
- NCBI tax ID: 1069161
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Vogesella fluminis KCTC 23713 | GCA_014652335 | contig | ncbi | 1069161 |
| 66792 | Vogesella fluminis strain KCTC 23713 | 1069161.3 | wgs | patric | 1069161 |
GC content
- @ref: 22490
- GC-content: 65.3
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 93.204 | yes |
| flagellated | yes | 93.555 | no |
| gram-positive | no | 98.595 | yes |
| anaerobic | no | 96.285 | yes |
| aerobic | yes | 75.646 | yes |
| halophile | no | 93.252 | yes |
| spore-forming | no | 95.131 | yes |
| thermophile | no | 96.452 | yes |
| glucose-util | yes | 79.683 | no |
| glucose-ferment | no | 89.986 | yes |
External links
@ref: 22490
culture collection no.: DSM 100851, BCRC 80377, KCTC 23713, LMG 26669
straininfo link
- @ref: 89707
- straininfo: 378086
literature
- topic: Phylogeny
- Pubmed-ID: 23396722
- title: Vogesella fluminis sp. nov., isolated from a freshwater river, and emended description of the genus Vogesella.
- authors: Sheu SY, Chen JC, Young CC, Chen WM
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.048629-0
- year: 2013
- mesh: Bacterial Typing Techniques, Base Composition, Betaproteobacteria/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Taiwan, *Water Microbiology
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |||
| 22490 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100851 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100851) | |||
| 30966 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27296 | 28776041 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 68369 | Automatically annotated from API 20NE | |||||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
| 89707 | Reimer, 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 identifiers | 10.60712/SI-ID378086.1 |