Strain identifier

BacDive ID: 5015

Type strain: Yes

Species: Pantoea brenneri

Strain Designation: BD 873

Strain history: <- T. Coutinho, Forestry and Agricultural Biotechnology Inst., Univ. Pretoria, South Africa; BD 873

NCBI tax ID(s): 472694 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 17572

BacDive-ID: 5015

DSM-Number: 24232

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

description: Pantoea brenneri BD 873 is a mesophilic bacterium that was isolated from human urethra.

NCBI tax id

  • NCBI tax id: 472694
  • Matching level: species

strain history

  • @ref: 17572
  • history: <- T. Coutinho, Forestry and Agricultural Biotechnology Inst., Univ. Pretoria, South Africa; BD 873

doi: 10.13145/bacdive5015.20230509.8.1

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

@ref: 17572

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Erwiniaceae

genus: Pantoea

species: Pantoea brenneri

full scientific name: Pantoea brenneri Brady et al. 2010

strain designation: BD 873

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17572COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
17572NUTRIENT 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

culture temp

@refgrowthtypetemperaturerange
17572positivegrowth30mesophilic
17572positivegrowth28mesophilic

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
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
6836815688acetoinno
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
17572+---+-----++++-++++++

Isolation, sampling and environmental information

isolation

  • @ref: 17572
  • sample type: human urethra
  • geographic location: Montana
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Urogenital tract#Urethra
#Infection#Patient

taxonmaps

  • @ref: 69479
  • File name: preview.99_996.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_310;97_507;98_583;99_996&stattab=map
  • Last taxonomy: Pantoea
  • 16S sequence: FJ611808
  • Sequence Identity:
  • Total samples: 7737
  • soil counts: 442
  • aquatic counts: 948
  • animal counts: 4423
  • plant counts: 1924

Safety information

risk assessment

  • @ref: 17572
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pantoea brenneri strain LMG 5343 16S ribosomal RNA gene, partial sequenceFJ6118081376ena472694
17572Pantoea brenneri strain LMG 5343 16S ribosomal RNA gene, partial sequenceEU2167351344ena472694

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pantoea brenneri LMG 5343GCA_002095305contigncbi472694
66792Pantoea brenneri strain LMG 5343472694.3wgspatric472694
66792Pantoea brenneri LMG 53432791355168draftimg472694

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno97.994no
anaerobicno98.602no
halophileno86.944no
spore-formingno94.445no
glucose-utilyes94.851no
aerobicno57.458no
flagellatedno67.091no
thermophileno99.062no
motileyes90.213no
glucose-fermentyes89.51yes

External links

@ref: 17572

culture collection no.: DSM 24232, LMG 5343

straininfo link

  • @ref: 74510
  • straininfo: 3812

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/urltitlejournalpubmed
17572Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24232)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24232
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
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
74510Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3812.1StrainInfo: A central database for resolving microbial strain identifiers