Strain identifier
BacDive ID: 23016
Type strain: 
Species: Phaseolibacter flectens
Strain history: <- NCPPB <- J. C. Johnson
NCBI tax ID(s): 1336237 (strain), 86187 (species)
version 9.1 (current version)
General
@ref: 19204
BacDive-ID: 23016
DSM-Number: 27043
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-negative, motile, rod-shaped
description: Phaseolibacter flectens DSM 27043 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from French bean Phaseolus vulgaris.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 86187 | species |
| 1336237 | strain |
strain history
- @ref: 19204
- history: <- NCPPB <- J. C. Johnson
doi: 10.13145/bacdive23016.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Enterobacterales
- family: Erwiniaceae
- genus: Phaseolibacter
- species: Phaseolibacter flectens
- full scientific name: Phaseolibacter flectens (Johnson 1956) Halpern et al. 2013
synonyms
- @ref: 20215
- synonym: Pseudomonas flectens
@ref: 19204
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Enterobacteriales, not validated
family: Erwiniaceae
genus: Phaseolibacter
species: Phaseolibacter flectens
full scientific name: Phaseolibacter flectens (Johnson 1956) Halpern et al. 2013
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 30332 | negative | 1.75 µm | 1.3 µm | rod-shaped | yes | |
| 69480 | negative | 97.994 |
pigmentation
- @ref: 30332
- production: yes
Culture and growth conditions
culture medium
- @ref: 19204
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 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 |
|---|---|---|---|
| 19204 | positive | growth | 28 |
| 30332 | positive | growth | 04-44 |
| 30332 | positive | optimum | 29 |
Physiology and metabolism
oxygen tolerance
- @ref: 30332
- oxygen tolerance: facultative anaerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69480 | no | 94.335 |
| 69481 | no | 100 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30332 | 22599 | arabinose | + | carbon source |
| 30332 | 16947 | citrate | + | carbon source |
| 30332 | 28757 | fructose | + | carbon source |
| 30332 | 33984 | fucose | + | carbon source |
| 30332 | 17234 | glucose | + | carbon source |
| 30332 | 17754 | glycerol | + | carbon source |
| 30332 | 33942 | ribose | + | carbon source |
| 30332 | 17992 | sucrose | + | carbon source |
| 30332 | 16296 | D-tryptophan | + | carbon source |
| 30332 | 18222 | xylose | + | carbon source |
| 30332 | 4853 | esculin | + | hydrolysis |
| 30332 | 17632 | nitrate | + | reduction |
enzymes
- @ref: 30332
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|---|
| 19204 | French bean Phaseolus vulgaris | Phaseolus vulgaris | Australia | AUS | Australia and Oceania | |
| 51222 | Phaseolus vulgaris | Australia | AUS | Australia and Oceania | 1956 |
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Herbaceous plants (Grass,Crops)
Safety information
risk assessment
- @ref: 19204
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19204
- description: Phaseolibacter flectens gene for 16S rRNA, strain: ATCC 12775
- accession: AB021400
- length: 1522
- database: nuccore
- NCBI tax ID: 1336237
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Phaseolibacter flectens ATCC 12775 | GCA_000518745 | scaffold | ncbi | 1336237 |
| 66792 | Pseudomonas flectens ATCC 12775 | 1336237.3 | wgs | patric | 1336237 |
| 66792 | Phaseolibacter flectens ATCC 12775 | 2545555808 | draft | img | 1336237 |
GC content
- @ref: 30332
- GC-content: 44.3
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 97.994 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.196 | yes |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 63.776 | yes |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 94.335 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 98 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 57.386 | no |
External links
@ref: 19204
culture collection no.: DSM 27043, ATCC 12775, CFBP 3281, ICMP 745, LMG 2187, NCPPB 539, CCUG 32859
straininfo link
- @ref: 87256
- straininfo: 4052
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 22407791 | Transfer of Pseudomonas flectens Johnson 1956 to Phaseolibacter gen. nov., in the family Enterobacteriaceae, as Phaseolibacter flectens gen. nov., comb. nov. | Halpern M, Fridman S, Aizenberg-Gershtein Y, Izhaki I | Int J Syst Evol Microbiol | 10.1099/ijs.0.033654-0 | 2012 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Enterobacteriaceae/*classification/genetics, Fatty Acids/analysis, Genes, Bacterial, Molecular Sequence Data, Phenotype, *Phylogeny, Pseudomonas/classification/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
| Phylogeny | 23832968 | Rosenbergiella nectarea gen. nov., sp. nov., in the family Enterobacteriaceae, isolated from floral nectar. | Halpern M, Fridman S, Atamna-Ismaeel N, Izhaki I | Int J Syst Evol Microbiol | 10.1099/ijs.0.052217-0 | 2013 | Bacterial Typing Techniques, Base Composition, Citrus/microbiology, DNA, Bacterial/genetics, Enterobacteriaceae/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Flowers/*microbiology, Genes, Bacterial, Israel, Molecular Sequence Data, *Phylogeny, *Plant Nectar, Prunus/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
| Genetics | 26767091 | High quality permanent draft genome sequence of Phaseolibacter flectens ATCC 12775(T), a plant pathogen of French bean pods. | Aizenberg-Gershtein Y, Izhaki I, Lapidus A, Copeland A, Reddy T, Huntemann M, Pillay M, Markowitz V, Goker M, Woyke T, Klenk HP, Kyrpides NC, Halpern M | Stand Genomic Sci | 10.1186/s40793-015-0127-5 | 2016 |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 19204 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27043) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-27043 | |||
| 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 | |||
| 30332 | 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 | 26673 | 28776041 | |
| 51222 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 32859) | https://www.ccug.se/strain?id=32859 | |||
| 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) | |||
| 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 | |||
| 87256 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID4052.1 | StrainInfo: A central database for resolving microbial strain identifiers |