Strain identifier
BacDive ID: 168636
Type strain: 
Species: Piscinibacter gummiphilus
Strain Designation: NS21
NCBI tax ID(s): 946333 (species)
version 9.1 (current version)
General
@ref: 20215
BacDive-ID: 168636
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Piscinibacter gummiphilus NS21 is a Gram-negative bacterium of the family Burkholderiales, not assigned to family.
NCBI tax id
- NCBI tax id: 946333
- Matching level: species
doi: 10.13145/bacdive168636.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Burkholderiales, not assigned to family
- genus: Piscinibacter
- species: Piscinibacter gummiphilus
- full scientific name: Piscinibacter gummiphilus (Imai et al. 2016) Liu et al. 2023
synonyms
- @ref: 20215
- synonym: Rhizobacter gummiphilus
@ref: 20215
domain: Bacteria
phylum: Pseudomonadota
class: Gammaproteobacteria
order: Pseudomonadales
family: Pseudomonadaceae
genus: Rhizobacter
species: Rhizobacter gummiphilus
full scientific name: Rhizobacter gummiphilus Imai et al. 2016
strain designation: NS21
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 97.8
Isolation, sampling and environmental information
taxonmaps
- @ref: 69479
- File name: preview.99_3981.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_818;97_2436;98_3013;99_3981&stattab=map
- Last taxonomy: Rhizobacter gummiphilus
- 16S sequence: AB609313
- Sequence Identity:
- Total samples: 504
- soil counts: 186
- aquatic counts: 125
- animal counts: 34
- plant counts: 159
Safety information
risk assessment
- @ref: 20215
- biosafety level: 1
- biosafety level comment: Risk group
Sequence information
16S sequences
- @ref: 20215
- description: Rhizobacter gummiphilus gene for 16S ribosomal RNA, partial sequence
- accession: AB609313
- length: 1447
- database: nuccore
- NCBI tax ID: 946333
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Rhizobacter gummiphilus NS21 | GCA_002116905 | complete | ncbi | 946333 |
| 66792 | Rhizobacter gummiphilus NBRC 109400 | GCA_002762215 | complete | ncbi | 946333 |
| 66792 | Rhizobacter gummiphilus strain NBRC 109400 | 946333.4 | complete | patric | 946333 |
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 97.8 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 96.399 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 89.119 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 89.263 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 98.429 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 82.134 | no |
External links
@ref: 20215
culture collection no.: NBRC 109400, BCC 58006
literature
- topic: Phylogeny
- Pubmed-ID: 23863290
- title: Rhizobacter gummiphilus sp. nov., a rubber-degrading bacterium isolated from the soil of a botanical garden in Japan.
- authors: Imai S, Yoshida R, Endo Y, Fukunaga Y, Yamazoe A, Kasai D, Masai E, Fukuda M
- journal: J Gen Appl Microbiol
- DOI: 10.2323/jgam.59.199
- year: 2013
- mesh: Aerobiosis, Anaerobiosis, Bacterial Typing Techniques, Base Composition, Biotransformation, Cluster Analysis, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flagella/physiology, Japan, Locomotion, Microscopy, Electron, Transmission, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pseudomonadaceae/*classification/genetics/*isolation & purification/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, *Rubber, Sequence Analysis, DNA, *Soil Microbiology
- topic2: Genetics
Reference
| @id | authors | title | doi/url |
|---|---|---|---|
| 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 |
| 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 |
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ |
| 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 |