Strain identifier
BacDive ID: 130231
Type strain: 
Species: Paraburkholderia aspalathi
Strain Designation: VG1C
Strain history: <- N. Mavengere, Dept. Botany and Zoology, Stellenbosch Univ., South Africa
NCBI tax ID(s): 1324617 (species)
version 9.3 (current version)
General
@ref: 21542
BacDive-ID: 130231
DSM-Number: 27239
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Paraburkholderia aspalathi VG1C is a mesophilic, Gram-negative bacterium that was isolated from root nodules of Aspalathus abietina Thunb..
NCBI tax id
- NCBI tax id: 1324617
- Matching level: species
strain history
- @ref: 21542
- history: <- N. Mavengere, Dept. Botany and Zoology, Stellenbosch Univ., South Africa
doi: 10.13145/bacdive130231.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Burkholderiaceae
- genus: Paraburkholderia
- species: Paraburkholderia aspalathi
- full scientific name: Paraburkholderia aspalathi (Mavengere et al. 2014) Sawana et al. 2017
synonyms
- @ref: 20215
- synonym: Burkholderia aspalathi
@ref: 21542
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Burkholderiaceae
genus: Paraburkholderia
species: Paraburkholderia aspalathi
full scientific name: Paraburkholderia aspalathi (Mavengere et al. 2014) Sawana et al. 2017
strain designation: VG1C
type strain: yes
Morphology
cell morphology
- @ref: 125438
- gram stain: negative
- confidence: 96.451
colony morphology
- @ref: 21542
- type of hemolysis: gamma
- incubation period: 2-3 days
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 21542 | CASO AGAR (MERCK 105458) (DSMZ Medium 220) | yes | https://mediadive.dsmz.de/medium/220 | Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water |
| 21542 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 21542 | positive | growth | 30 |
| 21542 | positive | growth | 28 |
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: obligate aerobe
- confidence: 98.1
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 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 | 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: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 21542 | catalase | + | 1.11.1.6 |
| 21542 | cytochrome-c oxidase | + | 1.9.3.1 |
| 68369 | gelatinase | - | |
| 68369 | urease | - | 3.5.1.5 |
| 68369 | cytochrome oxidase | + | 1.9.3.1 |
| 68369 | beta-glucosidase | - | 3.2.1.21 |
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 21542 | - | - | - | - | - | - | - | + | + | +/- | + | + | + | - | + | + | + | + | + | + | |
| 21542 | - | - | - | - | - | - | - | + | + | +/- | + | + | + | - | + | + | + | + | + | + | + |
Isolation, sampling and environmental information
isolation
- @ref: 21542
- sample type: root nodules of Aspalathus abietina Thunb.
- host species: Aspalathus abietina
- geographic location: Western Cape Province, Helderberg area, Vergelegen Wine Estate (34.05462° S 18.9367° E)
- country: South Africa
- origin.country: ZAF
- continent: Africa
- latitude: -34.0546
- longitude: 18.9366
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Root nodule |
Safety information
risk assessment
- @ref: 21542
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 21542
- description: Burkholderia aspalathi strain VG1C 16S ribosomal RNA gene, partial sequence
- accession: KC817488
- length: 1409
- database: nuccore
- NCBI tax ID: 1324617
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Paraburkholderia aspalathi LMG 27731 | GCA_900116445 | scaffold | ncbi | 1324617 |
| 66792 | Paraburkholderia aspalathi strain LMG 27731 | 1324617.3 | wgs | patric | 1324617 |
| 66792 | Paraburkholderia aspalathi LMG 27731 | 2671180117 | draft | img | 1324617 |
GC content
- @ref: 21542
- GC-content: 60.1
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 96.451 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 95.882 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 87.002 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 86.343 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 97.486 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 83.611 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 87.7 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 60.2 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 68.2 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate aerobe | 98.1 |
External links
@ref: 21542
culture collection no.: DSM 27239, LMG 27731
straininfo link
- @ref: 88773
- straininfo: 390418
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24599894 | Burkholderia aspalathi sp. nov., isolated from root nodules of the South African legume Aspalathus abietina Thunb. | Mavengere NR, Ellis AG, Le Roux JJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.057067-0 | 2014 | Aspalathus/*microbiology, Bacterial Typing Techniques, Base Composition, Burkholderia/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rec A Recombinases/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, South Africa, Ubiquinone/chemistry | Genetics |
| Phylogeny | 27469334 | Paraburkholderia caffeinilytica sp. nov., isolated from the soil of a tea plantation. | Gao Z, Yuan Y, Xu L, Liu R, Chen M, Zhang C | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001333 | 2016 | Bacterial Typing Techniques, Base Composition, Camellia/*microbiology, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry | Transcriptome |
| Phylogeny | 32027304 | Paraburkholderia madseniana sp. nov., a phenolic acid-degrading bacterium isolated from acidic forest soil. | Wilhelm RC, Murphy SJL, Feriancek NM, Karasz DC, DeRito CM, Newman JD, Buckley DH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004029 | 2020 | Bacterial Typing Techniques, Base Composition, Burkholderiaceae/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Hydroxybenzoates/*metabolism, New York, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry | Transcriptome |
| Phylogeny | 32809929 | Paraburkholderia solitsugae sp. nov. and Paraburkholderia elongata sp. nov., phenolic acid-degrading bacteria isolated from forest soil and emended description of Paraburkholderia madseniana. | Wilhelm RC, Cyle KT, Martinez CE, Karasz DC, Newman JD, Buckley DH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004387 | 2020 | Bacterial Typing Techniques, Base Composition, Burkholderiaceae/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Hydroxybenzoates, New York, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 21542 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27239 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27239) | |
| 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 | |||
| 88773 | 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-ID390418.1 | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |