Strain identifier
BacDive ID: 5017
Type strain:
Species: Pantoea allii
Strain Designation: BD390
Strain history: <- LMG <- I. Cleenwerck, Univ. Ghent, Belgium <- T. Coutinho, Forestry and Agricultural Biotechnology Inst., Univ. Pretoria, South Africa <- T. Goszczynska, Plant Protection Research Institute, Agricultural Research Council, Pretoria, South Africa
NCBI tax ID(s): 574096 (species)
General
@ref: 17915
BacDive-ID: 5017
DSM-Number: 25133
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped, plant pathogen
description: Pantoea allii BD390 is a facultative anaerobe, mesophilic, Gram-negative plant pathogen that was isolated from onion seed.
NCBI tax id
- NCBI tax id: 574096
- Matching level: species
strain history
- @ref: 17915
- history: <- LMG <- I. Cleenwerck, Univ. Ghent, Belgium <- T. Coutinho, Forestry and Agricultural Biotechnology Inst., Univ. Pretoria, South Africa <- T. Goszczynska, Plant Protection Research Institute, Agricultural Research Council, Pretoria, South Africa
doi: 10.13145/bacdive5017.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Enterobacterales
- family: Erwiniaceae
- genus: Pantoea
- species: Pantoea allii
- full scientific name: Pantoea allii Brady et al. 2011
@ref: 17915
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Enterobacteriales, not validated
family: Erwiniaceae
genus: Pantoea
species: Pantoea allii
full scientific name: Pantoea allii Brady et al. 2011
strain designation: BD390
type strain: yes
Morphology
cell morphology
- @ref: 29859
- gram stain: negative
- cell shape: rod-shaped
- motility: yes
pigmentation
- @ref: 29859
- production: yes
Culture and growth conditions
culture medium
- @ref: 17915
- 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 |
---|---|---|---|---|
17915 | positive | growth | 28 | mesophilic |
29859 | positive | growth | 30-40 |
Physiology and metabolism
oxygen tolerance
- @ref: 29859
- oxygen tolerance: facultative anaerobe
spore formation
- @ref: 29859
- spore formation: no
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29859 | 16808 | 2-dehydro-D-gluconate | + | carbon source |
29859 | 58143 | 5-dehydro-D-gluconate | + | carbon source |
29859 | 30089 | acetate | + | carbon source |
29859 | 15963 | ribitol | + | carbon source |
29859 | 16449 | alanine | + | carbon source |
29859 | 22599 | arabinose | + | carbon source |
29859 | 18403 | L-arabitol | + | carbon source |
29859 | 22653 | asparagine | + | carbon source |
29859 | 35391 | aspartate | + | carbon source |
29859 | 17057 | cellobiose | + | carbon source |
29859 | 16947 | citrate | + | carbon source |
29859 | 23652 | dextrin | + | carbon source |
29859 | 28757 | fructose | + | carbon source |
29859 | 28260 | galactose | + | carbon source |
29859 | 24175 | galacturonate | + | carbon source |
29859 | 24265 | gluconate | + | carbon source |
29859 | 5417 | glucosamine | + | carbon source |
29859 | 17234 | glucose | + | carbon source |
29859 | 29987 | glutamate | + | carbon source |
29859 | 17754 | glycerol | + | carbon source |
29859 | 24996 | lactate | + | carbon source |
29859 | 17716 | lactose | + | carbon source |
29859 | 25115 | malate | + | carbon source |
29859 | 17306 | maltose | + | carbon source |
29859 | 37684 | mannose | + | carbon source |
29859 | 28053 | melibiose | + | carbon source |
29859 | 17268 | myo-inositol | + | carbon source |
29859 | 506227 | N-acetylglucosamine | + | carbon source |
29859 | 26271 | proline | + | carbon source |
29859 | 51850 | methyl pyruvate | + | carbon source |
29859 | 26490 | quinate | + | carbon source |
29859 | 16634 | raffinose | + | carbon source |
29859 | 26546 | rhamnose | + | carbon source |
29859 | 33942 | ribose | + | carbon source |
29859 | 17822 | serine | + | carbon source |
29859 | 30911 | sorbitol | + | carbon source |
29859 | 30031 | succinate | + | carbon source |
29859 | 17992 | sucrose | + | carbon source |
29859 | 27082 | trehalose | + | carbon source |
29859 | 53423 | tween 40 | + | carbon source |
29859 | 53426 | tween 80 | + | carbon source |
29859 | 18222 | xylose | + | carbon source |
metabolite production
- @ref: 29859
- Chebi-ID: 35581
- metabolite: indole
- production: yes
metabolite tests
- @ref: 29859
- Chebi-ID: 35581
- metabolite: indole
- indole test: +
enzymes
- @ref: 29859
- value: catalase
- activity: +
- ec: 1.11.1.6
Isolation, sampling and environmental information
isolation
- @ref: 17915
- sample type: onion seed
- country: South Africa
- origin.country: ZAF
- continent: Africa
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Herbaceous plants (Grass,Crops)
taxonmaps
- @ref: 69479
- File name: preview.99_727.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_310;97_507;98_583;99_727&stattab=map
- Last taxonomy: Pantoea ananatis
- 16S sequence: AY530795
- Sequence Identity:
- Total samples: 8803
- soil counts: 845
- aquatic counts: 764
- animal counts: 5045
- plant counts: 2149
Safety information
risk assessment
- @ref: 17915
- pathogenicity plant: yes
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17915
- description: Pantoea allii strain BD 390 16S ribosomal RNA gene, partial sequence
- accession: AY530795
- length: 1533
- database: ena
- NCBI tax ID: 574096
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pantoea allii LMG 24248 | GCA_002307475 | contig | ncbi | 574096 |
66792 | Pantoea allii LMG 24248 | GCA_002095545 | contig | ncbi | 574096 |
66792 | Pantoea allii strain LMG 24248 | 574096.3 | wgs | patric | 574096 |
66792 | Pantoea allii strain LMG 24248 | 574096.6 | wgs | patric | 574096 |
66792 | Pantoea allii LMG 24248 | 2814123165 | draft | img | 574096 |
GC content
- @ref: 29859
- GC-content: 53.6
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
gram-positive | no | 97.881 | yes |
anaerobic | no | 99.068 | yes |
halophile | no | 80.181 | no |
spore-forming | no | 93.913 | yes |
glucose-util | yes | 95.638 | no |
thermophile | no | 99.119 | yes |
flagellated | no | 64.844 | no |
aerobic | no | 62.678 | yes |
motile | yes | 91.399 | yes |
glucose-ferment | yes | 89.627 | no |
External links
@ref: 17915
culture collection no.: DSM 25133, LMG 24248
straininfo link
- @ref: 74512
- straininfo: 281218
literature
- topic: Phylogeny
- Pubmed-ID: 20495023
- title: Pantoea allii sp. nov., isolated from onion plants and seed.
- authors: Brady CL, Goszczynska T, Venter SN, Cleenwerck I, De Vos P, Gitaitis RD, Coutinho TA
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.022921-0
- year: 2010
- mesh: Aerobiosis, Amplified Fragment Length Polymorphism Analysis, Amygdalin/metabolism, Anaerobiosis, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Locomotion, Molecular Sequence Data, Multilocus Sequence Typing, Nucleic Acid Hybridization, Onions/*microbiology, Oxidoreductases/metabolism, Pantoea/*classification/genetics/*isolation & purification/physiology, Phylogeny, Pigments, Biological/metabolism, Plant Diseases/microbiology, RNA, Ribosomal, 16S/genetics, Ribitol/metabolism, Seeds/*microbiology, Sequence Analysis, DNA, Sorbitol/metabolism, South Africa, United States
- topic2: Metabolism
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
17915 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25133) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25133 | |||
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 | |||
29859 | 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 | 26233 | 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) | |||
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 | |||
74512 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID281218.1 | StrainInfo: A central database for resolving microbial strain identifiers |