Strain identifier
BacDive ID: 5009
Type strain:
Species: Pantoea deleyi
Strain Designation: BD 767, R-31523
Strain history: <- T. Coutinho, Forestry and Agricultural Biotechnology Inst., Univ. Pretoria, South Africa; R-31523
NCBI tax ID(s): 470932 (species)
General
@ref: 16696
BacDive-ID: 5009
DSM-Number: 23079
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Pantoea deleyi BD 767 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from Eucalyptus.
NCBI tax id
- NCBI tax id: 470932
- Matching level: species
strain history
- @ref: 16696
- history: <- T. Coutinho, Forestry and Agricultural Biotechnology Inst., Univ. Pretoria, South Africa; R-31523
doi: 10.13145/bacdive5009.20230509.8.1
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 deleyi
- full scientific name: Pantoea deleyi Brady et al. 2009
@ref: 16696
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Enterobacteriales, not validated
family: Erwiniaceae
genus: Pantoea
species: Pantoea deleyi
full scientific name: Pantoea deleyi Brady et al. 2009
strain designation: BD 767, R-31523
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29239 | negative | 1.5-3.0 µm | 0.9 µm | rod-shaped | yes | |
69480 | yes | 97.542 | ||||
69480 | negative | 99.987 |
multimedia
- @ref: 16696
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_23079.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 16696
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
- @ref: 16696
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 29239
- oxygen tolerance: facultative anaerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
29239 | no | |
69481 | no | 100 |
69480 | no | 99.934 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29239 | 16449 | alanine | + | carbon source |
29239 | 22599 | arabinose | + | carbon source |
29239 | 18403 | L-arabitol | + | carbon source |
29239 | 35391 | aspartate | + | carbon source |
29239 | 16947 | citrate | + | carbon source |
29239 | 28757 | fructose | + | carbon source |
29239 | 28260 | galactose | + | carbon source |
29239 | 17234 | glucose | + | carbon source |
29239 | 29987 | glutamate | + | carbon source |
29239 | 17754 | glycerol | + | carbon source |
29239 | 15792 | malonate | + | carbon source |
29239 | 17306 | maltose | + | carbon source |
29239 | 29864 | mannitol | + | carbon source |
29239 | 37684 | mannose | + | carbon source |
29239 | 26271 | proline | + | carbon source |
29239 | 26546 | rhamnose | + | carbon source |
29239 | 33942 | ribose | + | carbon source |
29239 | 17822 | serine | + | carbon source |
29239 | 30031 | succinate | + | carbon source |
29239 | 17992 | sucrose | + | carbon source |
29239 | 27082 | trehalose | + | carbon source |
29239 | 53423 | tween 40 | + | carbon source |
29239 | 53426 | tween 80 | + | carbon source |
29239 | 18222 | xylose | + | carbon source |
Isolation, sampling and environmental information
isolation
- @ref: 16696
- sample type: Eucalyptus
- country: Uganda
- origin.country: UGA
- continent: Africa
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Tree
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: AY173023
- Sequence Identity:
- Total samples: 8803
- soil counts: 845
- aquatic counts: 764
- animal counts: 5045
- plant counts: 2149
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Pantoea ananatis strain BCC0109 16S ribosomal RNA gene, partial sequence | AY173023 | 1325 | ena | 553 |
16696 | Pantoea deleyi strain LMG 24200 16S ribosomal RNA gene, partial sequence | EF688011 | 1443 | ena | 470932 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pantoea deleyi LMG 24200 | GCA_006494415 | contig | ncbi | 470932 |
66792 | Pantoea deleyi LMG 24200 | GCA_002095375 | contig | ncbi | 470932 |
66792 | Pantoea deleyi strain LMG 24200 | 470932.7 | wgs | patric | 470932 |
66792 | Pantoea deleyi strain LMG 24200 | 470932.3 | wgs | patric | 470932 |
66792 | Pantoea deleyi LMG 24200 | 2791355166 | draft | img | 470932 |
66792 | Pantoea deleyi LMG24200 | GCA_022647325 | complete | ncbi | 470932 |
GC content
@ref | GC-content | method |
---|---|---|
16696 | 58.6 | high performance liquid chromatography (HPLC) |
29239 | 58.6 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 69.385 | no |
gram-positive | no | 98.267 | yes |
anaerobic | no | 98.671 | yes |
aerobic | no | 74.662 | no |
halophile | no | 86.28 | no |
spore-forming | no | 95.337 | yes |
motile | yes | 92.508 | yes |
glucose-ferment | yes | 89.741 | no |
thermophile | no | 99.05 | no |
glucose-util | yes | 95.198 | yes |
External links
@ref: 16696
culture collection no.: DSM 23079, BCC 109, LMG 24200
straininfo link
- @ref: 74504
- straininfo: 265256
literature
- topic: Phylogeny
- Pubmed-ID: 19620357
- title: Pantoea vagans sp. nov., Pantoea eucalypti sp. nov., Pantoea deleyi sp. nov. and Pantoea anthophila sp. nov.
- authors: Brady CL, Venter SN, Cleenwerck I, Engelbeen K, Vancanneyt M, Swings J, Coutinho TA
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.009241-0
- year: 2009
- mesh: Amplified Fragment Length Polymorphism Analysis, Argentina, Bacterial Typing Techniques, Cluster Analysis, DNA Fingerprinting, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Eucalyptus/*microbiology, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Pantoea/*classification/genetics/*isolation & purification, Phylogeny, Plant Diseases/*microbiology, Plant Leaves/microbiology, Plant Shoots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, South Africa, Uganda, Uruguay, Zea mays/*microbiology
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
16696 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23079) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23079 | ||||
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 | ||||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | ||
29239 | 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 | 28776041 | 25659 | ||
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 | ||||
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 | ||||
74504 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID265256.1 | StrainInfo: A central database for resolving microbial strain identifiers |