Strain identifier

BacDive ID: 5017

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refgrowthtypetemperaturerange
17915positivegrowth28mesophilic
29859positivegrowth30-40

Physiology and metabolism

oxygen tolerance

  • @ref: 29859
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 29859
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
29859168082-dehydro-D-gluconate+carbon source
29859581435-dehydro-D-gluconate+carbon source
2985930089acetate+carbon source
2985915963ribitol+carbon source
2985916449alanine+carbon source
2985922599arabinose+carbon source
2985918403L-arabitol+carbon source
2985922653asparagine+carbon source
2985935391aspartate+carbon source
2985917057cellobiose+carbon source
2985916947citrate+carbon source
2985923652dextrin+carbon source
2985928757fructose+carbon source
2985928260galactose+carbon source
2985924175galacturonate+carbon source
2985924265gluconate+carbon source
298595417glucosamine+carbon source
2985917234glucose+carbon source
2985929987glutamate+carbon source
2985917754glycerol+carbon source
2985924996lactate+carbon source
2985917716lactose+carbon source
2985925115malate+carbon source
2985917306maltose+carbon source
2985937684mannose+carbon source
2985928053melibiose+carbon source
2985917268myo-inositol+carbon source
29859506227N-acetylglucosamine+carbon source
2985926271proline+carbon source
2985951850methyl pyruvate+carbon source
2985926490quinate+carbon source
2985916634raffinose+carbon source
2985926546rhamnose+carbon source
2985933942ribose+carbon source
2985917822serine+carbon source
2985930911sorbitol+carbon source
2985930031succinate+carbon source
2985917992sucrose+carbon source
2985927082trehalose+carbon source
2985953423tween 40+carbon source
2985953426tween 80+carbon source
2985918222xylose+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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pantoea allii LMG 24248GCA_002307475contigncbi574096
66792Pantoea allii LMG 24248GCA_002095545contigncbi574096
66792Pantoea allii strain LMG 24248574096.3wgspatric574096
66792Pantoea allii strain LMG 24248574096.6wgspatric574096
66792Pantoea allii LMG 242482814123165draftimg574096

GC content

  • @ref: 29859
  • GC-content: 53.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno97.881yes
anaerobicno99.068yes
halophileno80.181no
spore-formingno93.913yes
glucose-utilyes95.638no
thermophileno99.119yes
flagellatedno64.844no
aerobicno62.678yes
motileyes91.399yes
glucose-fermentyes89.627no

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

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17915Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25133)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25133
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
29859Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2623328776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69479João 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
74512Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID281218.1StrainInfo: A central database for resolving microbial strain identifiers