Strain identifier

BacDive ID: 5011

Type strain: Yes

Species: Pantoea vagans

Strain Designation: BD 765, R-21566

Strain history: <- T. A. Coutinho, Forestry and Agricultural Biotechnology Inst., Univ. Pretoria, South Africa; R-21566

NCBI tax ID(s): 470934 (species)

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General

@ref: 16695

BacDive-ID: 5011

DSM-Number: 23078

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, plant pathogen

description: Pantoea vagans BD 765 is a facultative anaerobe, mesophilic, Gram-negative plant pathogen that was isolated from Eucalyptus sp..

NCBI tax id

  • NCBI tax id: 470934
  • Matching level: species

strain history

  • @ref: 16695
  • history: <- T. A. Coutinho, Forestry and Agricultural Biotechnology Inst., Univ. Pretoria, South Africa; R-21566

doi: 10.13145/bacdive5011.20230509.8.1

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 vagans
  • full scientific name: Pantoea vagans Brady et al. 2009

@ref: 16695

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Erwiniaceae

genus: Pantoea

species: Pantoea vagans

full scientific name: Pantoea vagans Brady et al. 2009

strain designation: BD 765, R-21566

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotilityconfidence
29239negative1.5-3.0 µm0.9 µmyes
69480yes97.606
69480negative99.986

Culture and growth conditions

culture medium

  • @ref: 16695
  • 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: 16695
  • 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
69480no99.963

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2923916449alanine+carbon source
2923922599arabinose+carbon source
2923935391aspartate+carbon source
2923917057cellobiose+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
29239506227N-acetylglucosamine+carbon source
2923918257ornithine+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
6836830849L-arabinose+fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose+fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol+fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68368cytochrome oxidase-1.9.3.1
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
16695+---+----+++++-++--+-

Isolation, sampling and environmental information

isolation

  • @ref: 16695
  • sample type: Eucalyptus sp.
  • host species: Eucalyptus
  • country: Uganda
  • origin.country: UGA
  • continent: Africa

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Shrub (Scrub)
#Host#Plants#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: AY173021
  • Sequence Identity:
  • Total samples: 8803
  • soil counts: 845
  • aquatic counts: 764
  • animal counts: 5045
  • plant counts: 2149

Safety information

risk assessment

  • @ref: 16695
  • pathogenicity plant: yes
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pantoea ananatis strain BCC0105 16S ribosomal RNA gene, partial sequenceAY1730211325ena553
16695Pantoea vagans strain LMG 24199 16S ribosomal RNA gene, partial sequenceEF6880121429ena470934

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pantoea vagans LMG 24199GCA_004792415completencbi470934
66792Pantoea vagans strain LMG 24199470934.52completepatric470934
66792Pantoea vagans LMG 241992844050306completeimg470934

GC content

@refGC-contentmethod
1669555.4high performance liquid chromatography (HPLC)
2923955.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes92.552yes
flagellatedno65.168no
gram-positiveno97.915no
anaerobicno98.821yes
aerobicno73.348yes
halophileno85.557no
spore-formingno94.136yes
glucose-utilyes95.356yes
thermophileno99.251no
glucose-fermentyes89.791yes

External links

@ref: 16695

culture collection no.: DSM 23078, BCC 105, LMG 24199

straininfo link

  • @ref: 74506
  • straininfo: 127387

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
16695Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23078)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23078
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)
68368Automatically annotated from API 20E
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
74506Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID127387.1StrainInfo: A central database for resolving microbial strain identifiers