Strain identifier

BacDive ID: 4393

Type strain: Yes

Species: Erwinia pyrifoliae

Strain Designation: Ep16/96, Ep 16/96

Strain history: CIP <- 1999, K. Geider, Max-Planck-Institut, Ladenburg, Germany <- S.-L. Rhim: strain Ep 16/96

NCBI tax ID(s): 644651 (strain), 79967 (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: 4558

BacDive-ID: 4393

DSM-Number: 12163

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile, plant pathogen

description: Erwinia pyrifoliae Ep16/96 is a mesophilic, motile plant pathogen that was isolated from Pyrus pyrifolia.

NCBI tax id

NCBI tax idMatching level
644651strain
79967species

strain history

@refhistory
4558<- K. Geider; Ep16/96 <- S.-L. Rhim
122091CIP <- 1999, K. Geider, Max-Planck-Institut, Ladenburg, Germany <- S.-L. Rhim: strain Ep 16/96

doi: 10.13145/bacdive4393.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Erwiniaceae
  • genus: Erwinia
  • species: Erwinia pyrifoliae
  • full scientific name: Erwinia pyrifoliae Kim et al. 1999

@ref: 4558

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Erwiniaceae

genus: Erwinia

species: Erwinia pyrifoliae

full scientific name: Erwinia pyrifoliae Kim et al. 1999

strain designation: Ep16/96, Ep 16/96

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.95
6948099.994negative
122091yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4558REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a)yeshttps://mediadive.dsmz.de/medium/220aName: REACTIVATION WITH TRYPTONE SOYA BROTH (DSMZ Medium 220a) Composition: Casein peptone 17.0 g/l Agar 15.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
39473MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122091CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
4558positivegrowth30mesophilic
39473positivegrowth25mesophilic
122091positivegrowth5-30
122091nogrowth37mesophilic
122091nogrowth41thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.969

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol+builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol+builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
122091mannitol-fermentation29864
122091citrate-carbon source16947
122091lactose-fermentation17716
122091nitrate-reduction17632
122091nitrite-reduction16301
122091malonate-assimilation15792
122091sodium thiosulfate-builds gas from132112
122091glucose+degradation17234

antibiotic resistance

  • @ref: 122091
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 122091
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12209115688acetoin+
12209117234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
122091oxidase-
122091beta-galactosidase-3.2.1.23
122091alcohol dehydrogenase-1.1.1.1
122091gelatinase-
122091catalase+1.11.1.6
122091lysine decarboxylase-4.1.1.18
122091ornithine decarboxylase-4.1.1.17
122091phenylalanine ammonia-lyase+4.3.1.24
122091tryptophan deaminase-
122091urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122091-+++-+++--++---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122091+/---++----+++----+++--+--------++-----------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122091++++---+---------+-++----------+++--+------------+---------++------------------++--------+++-++----

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentisolation date
4558Pyrus pyrifoliaPyrus pyrifoliaRepublic of KoreaKORAsia
122091Necrotic tissue of Nashi pearRepublic of KoreaKORAsia1996

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Tree

taxonmaps

  • @ref: 69479
  • File name: preview.99_717.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_502;98_576;99_717&stattab=map
  • Last taxonomy: Erwinia
  • 16S sequence: AM980502
  • Sequence Identity:
  • Total samples: 2160
  • soil counts: 90
  • aquatic counts: 255
  • animal counts: 1537
  • plant counts: 278

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
4558yes1Risk group (German classification)
1220911Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Erwinia pyrifoliae gene for 16S ribosomal RNA, partial sequence, strain: DSM12163AB2428801110ena644651
20218Erwinia pyrifoliae partial 16S rRNA gene, strain Ep16/96AM9805021349ena79967
20218Erwinia pyrifoliae DSM 12163 16S ribosomal RNA gene, partial sequenceFJ6118571387ena644651

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Erwinia pyrifoliae DSM 12163GCA_000026985chromosomencbi644651
66792Erwinia pyrifoliae DSM 12163644651.11plasmidpatric644651
66792Erwinia pyrifoliae DSM 12163644651.3completepatric644651
66792Erwinia pyrifoliae DSM 12163644651.13plasmidpatric644651
66792Erwinia pyrifoliae DSM 12163644651.12plasmidpatric644651
66792Erwinia pyrifoliae DSM 12163644651.14plasmidpatric644651
66792Erwinia pyrifoliae DSM 12163646862321completeimg644651

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.544no
anaerobicno98.276no
halophileno78.716no
spore-formingno96.183no
glucose-utilyes96.495no
thermophileno97.853yes
flagellatedno59.792no
aerobicno54.164no
motileyes91.033no
glucose-fermentyes86.637no

External links

@ref: 4558

culture collection no.: DSM 12163, CIP 106111, CFBP 4172

straininfo link

  • @ref: 73884
  • straininfo: 49243

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10319516Erwinia pyrifoliae sp. nov., a novel pathogen that affects Asian pear trees (Pyrus pyrifolia Nakai)Kim WS, Gardan L, Rhim SL, Geider KInt J Syst Bacteriol10.1099/00207713-49-2-8991999Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Erwinia/*classification/*genetics/isolation & purification, Fruit, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Plant Diseases/microbiology, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Rosales/*microbiology, Sequence Analysis, DNAGenetics
Genetics20047678Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163T and comparative genomic insights into plant pathogenicity.Smits TH, Jaenicke S, Rezzonico F, Kamber T, Goesmann A, Frey JE, Duffy BBMC Genomics10.1186/1471-2164-11-22010Comparative Genomic Hybridization, DNA, Bacterial/genetics, Erwinia/*genetics/pathogenicity, *Genome, Bacterial, Genomic Islands, Molecular Sequence Data, Plant Diseases/*microbiology, Plasmids, Sequence Analysis, DNA, Software, Virulence Factors/geneticsTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4558Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12163)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12163
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
39473Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18206
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)
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
73884Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49243.1StrainInfo: A central database for resolving microbial strain identifiers
122091Curators of the CIPCollection of Institut Pasteur (CIP 106111)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106111