Strain identifier

BacDive ID: 5014

Type strain: Yes

Species: Pantoea eucrina

Strain Designation: BD 872

Strain history: <- T. Coutinho, Forestry and Agricultural Biotechnology Inst., Univ. Pretoria, South Africa; BD 872 <- P. Grimont, CDC, Paris, France

NCBI tax ID(s): 472693 (species)

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General

@ref: 17571

BacDive-ID: 5014

DSM-Number: 24231

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Pantoea eucrina BD 872 is a mesophilic bacterium that was isolated from human trachea.

NCBI tax id

  • NCBI tax id: 472693
  • Matching level: species

strain history

  • @ref: 17571
  • history: <- T. Coutinho, Forestry and Agricultural Biotechnology Inst., Univ. Pretoria, South Africa; BD 872 <- P. Grimont, CDC, Paris, France

doi: 10.13145/bacdive5014.20230509.8.1

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 eucrina
  • full scientific name: Pantoea eucrina Brady et al. 2010

@ref: 17571

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Erwiniaceae

genus: Pantoea

species: Pantoea eucrina

full scientific name: Pantoea eucrina Brady et al. 2010

strain designation: BD 872

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17571NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
17571COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium693.pdf
17571TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium92.pdf

culture temp

@refgrowthtypetemperaturerange
17571positivegrowth28mesophilic
17571positivegrowth30mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose+fermentation
6836827613amygdalin-fermentation
6836828053melibiose+fermentation
6836817992sucrose+fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-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
17571+---+----+-+++/---++-++

Isolation, sampling and environmental information

isolation

  • @ref: 17571
  • sample type: human trachea
  • geographic location: Connecticut
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Oral cavity and airways#Trachea

taxonmaps

  • @ref: 69479
  • File name: preview.99_4237.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_651;98_3191;99_4237&stattab=map
  • Last taxonomy: Erwiniaceae
  • 16S sequence: EU216736
  • Sequence Identity:
  • Total samples: 8794
  • soil counts: 617
  • aquatic counts: 1100
  • animal counts: 4755
  • plant counts: 2322

Safety information

risk assessment

  • @ref: 17571
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17571
  • description: Pantoea eucrina strain LMG 2781 16S ribosomal RNA gene, partial sequence
  • accession: EU216736
  • length: 1344
  • database: ena
  • NCBI tax ID: 472693

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pantoea eucrina LMG 5346GCA_002095385contigncbi472693
66792Pantoea eucrina strain LMG 5346472693.6wgspatric472693

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno97.804no
anaerobicno98.919no
halophileno80.835no
spore-formingno94.943no
glucose-utilyes95.422no
aerobicno58.022no
flagellatedno50no
thermophileno98.9yes
motileyes93.202no
glucose-fermentyes88.18yes

External links

@ref: 17571

culture collection no.: DSM 24231, LMG 2781, LMG 5346

straininfo link

  • @ref: 74509
  • straininfo: 6612

literature

  • topic: Phylogeny
  • Pubmed-ID: 19946052
  • title: Emended description of the genus Pantoea, description of four species from human clinical samples, Pantoea septica sp. nov., Pantoea eucrina sp. nov., Pantoea brenneri sp. nov. and Pantoea conspicua sp. nov., and transfer of Pectobacterium cypripedii (Hori 1911) Brenner et al. 1973 emend. Hauben et al. 1998 to the genus as Pantoea cypripedii comb. nov.
  • authors: Brady CL, Cleenwerck I, Venter SN, Engelbeen K, De Vos P, Coutinho TA
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.017301-0
  • year: 2009
  • mesh: Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Enterobacteriaceae Infections/*microbiology, Humans, Molecular Sequence Data, Multilocus Sequence Typing, Nucleic Acid Hybridization, Pantoea/*classification/*isolation & purification, Pectobacterium/*classification/*isolation & purification, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitle
17571Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24231)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24231
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
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
74509Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID6612.1StrainInfo: A central database for resolving microbial strain identifiers