Strain identifier

BacDive ID: 5009

Type strain: Yes

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)

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

@refgram staincell lengthcell widthcell shapemotilityconfidence
29239negative1.5-3.0 µm0.9 µmrod-shapedyes
69480yes97.542
69480negative99.987

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

@refspore formationconfidence
29239no
69481no100
69480no99.934

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2923916449alanine+carbon source
2923922599arabinose+carbon source
2923918403L-arabitol+carbon source
2923935391aspartate+carbon source
2923916947citrate+carbon source
2923928757fructose+carbon source
2923928260galactose+carbon source
2923917234glucose+carbon source
2923929987glutamate+carbon source
2923917754glycerol+carbon source
2923915792malonate+carbon source
2923917306maltose+carbon source
2923929864mannitol+carbon source
2923937684mannose+carbon source
2923926271proline+carbon source
2923926546rhamnose+carbon source
2923933942ribose+carbon source
2923917822serine+carbon source
2923930031succinate+carbon source
2923917992sucrose+carbon source
2923927082trehalose+carbon source
2923953423tween 40+carbon source
2923953426tween 80+carbon source
2923918222xylose+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

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pantoea ananatis strain BCC0109 16S ribosomal RNA gene, partial sequenceAY1730231325ena553
16696Pantoea deleyi strain LMG 24200 16S ribosomal RNA gene, partial sequenceEF6880111443ena470932

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pantoea deleyi LMG 24200GCA_006494415contigncbi470932
66792Pantoea deleyi LMG 24200GCA_002095375contigncbi470932
66792Pantoea deleyi strain LMG 24200470932.7wgspatric470932
66792Pantoea deleyi strain LMG 24200470932.3wgspatric470932
66792Pantoea deleyi LMG 242002791355166draftimg470932
66792Pantoea deleyi LMG24200GCA_022647325completencbi470932

GC content

@refGC-contentmethod
1669658.6high performance liquid chromatography (HPLC)
2923958.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno69.385no
gram-positiveno98.267yes
anaerobicno98.671yes
aerobicno74.662no
halophileno86.28no
spore-formingno95.337yes
motileyes92.508yes
glucose-fermentyes89.741no
thermophileno99.05no
glucose-utilyes95.198yes

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

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
16696Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23079)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23079
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
29239Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604125659
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
74504Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265256.1StrainInfo: A central database for resolving microbial strain identifiers