Strain identifier

BacDive ID: 5025

Type strain: Yes

Species: Pectobacterium wasabiae

Strain Designation: SR91, SR 91

Strain history: CIP <- 1997, CFBP <- M. Goto: strain SR 91

NCBI tax ID(s): 1175631 (strain), 55208 (species)

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General

@ref: 7375

BacDive-ID: 5025

DSM-Number: 18074

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

description: Pectobacterium wasabiae SR91 is a facultative anaerobe, mesophilic, motile plant pathogen that was isolated from Eutrema wasabi.

NCBI tax id

NCBI tax idMatching level
55208species
1175631strain

strain history

@refhistory
7375<- CFBP <- ICMP <- M. Goto; SR91
123913CIP <- 1997, CFBP <- M. Goto: strain SR 91

doi: 10.13145/bacdive5025.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Pectobacteriaceae
  • genus: Pectobacterium
  • species: Pectobacterium wasabiae
  • full scientific name: Pectobacterium wasabiae (Goto and Matsumoto 1987) Gardan et al. 2003

  • synonyms

    @refsynonym
    20215Pectobacterium carotovorum subsp. wasabiae
    20215Erwinia carotovora subsp. wasabiae

@ref: 7375

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Pectobacteriaceae

genus: Pectobacterium

species: Pectobacterium wasabiae

full scientific name: Pectobacterium wasabiae (Goto and Matsumoto 1987) Gardan et al. 2003

strain designation: SR91, SR 91

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.527
6948099.997negative
123913yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7375REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
39223MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123913CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
7375positivegrowth28mesophilic
39223positivegrowth25mesophilic
123913positivegrowth10-25psychrophilic
123913nogrowth5psychrophilic
123913nogrowth37mesophilic
123913nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123913
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.973

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
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
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
68371glycerol+builds acid from17754
68368L-arabinose+fermentation30849
68368amygdalin+fermentation27613
68368melibiose-fermentation28053
68368sucrose+fermentation17992
68368L-rhamnose+fermentation62345
68368sorbitol-fermentation30911
68368myo-inositol+fermentation17268
68368D-mannitol+fermentation16899
68368D-glucose+fermentation17634
68368gelatin+hydrolysis5291
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368citrate+assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
123913mannitol+fermentation29864
123913citrate+carbon source16947
123913glucose+fermentation17234
123913lactose-fermentation17716
123913nitrate+reduction17632
123913nitrite+reduction16301
123913malonate-assimilation15792
123913sodium thiosulfate-builds gas from132112
123913glucose+degradation17234

antibiotic resistance

  • @ref: 123913
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12391335581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12391315688acetoin+
12391317234glucose+

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
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
123913oxidase-
123913beta-galactosidase-3.2.1.23
123913alcohol dehydrogenase-1.1.1.1
123913gelatinase+/-
123913catalase+1.11.1.6
123913lysine decarboxylase-4.1.1.18
123913ornithine decarboxylase-4.1.1.17
123913phenylalanine ammonia-lyase-4.3.1.24
123913tryptophan deaminase-
123913urease-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
123913-++--+--+-++----+---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
7375----+----+++++-++-++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123913+--+++---++++-+-++---++/-+++++/---++------+-------+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123913+++++--+-------+++++++-+-------+++---------++--+-+---+++---++--------------+---++-+---+--+---------

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentisolation date
7375Eutrema wasabiEutrema wasabiJapanJPNAsia
123913Japanese horseradish, Eutrema wasabiJapanJPNAsia1985

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
7375yes1Risk group (German classification)
1239131Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pectobacterium carotovorum subsp. wasabiae strain ATCC 43316 16S-23S intergenic spacer region and tRNA-Glu gene, complete sequenceAF232679448ena1175631
20218Pectobacterium wasabiae CFBP 3304 16S ribosomal RNA gene, partial sequenceU801991458ena1175631
7375Pectobacterium carotovorum subsp. wasabiae, strain ICMP 9121-T 16S rRNA geneAJ2234081498ena1175631

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pectobacterium wasabiae CFBP 3304GCA_001742185completencbi1175631
66792Pectobacterium wasabiae CFBP 3304GCA_000291725contigncbi1175631
66792Pectobacterium wasabiae CFBP 33041175631.8completepatric1175631
66792Pectobacterium wasabiae CFBP 33041175631.4wgspatric1175631
66792Pectobacterium wasabiae CFBP 33042537561728draftimg1175631

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes55.356no
gram-positiveno97.958no
anaerobicno96.983no
aerobicno50no
halophileno88.468no
spore-formingno93.248no
glucose-utilyes93.259no
thermophileno98.957no
motileyes91.951no
glucose-fermentyes91.992yes

External links

@ref: 7375

culture collection no.: DSM 18074, ATCC 43316, CIP 105194, CFBP 3304, ICMP 9121, LMG 8404, NCPPB 3701, PDDCC 9121

straininfo link

  • @ref: 74520
  • straininfo: 41768

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12710602Elevation of three subspecies of Pectobacterium carotovorum to species level: Pectobacterium atrosepticum sp. nov., Pectobacterium betavasculorum sp. nov. and Pectobacterium wasabiae sp. nov.Gardan L, Gouy C, Christen R, Samson RInt J Syst Evol Microbiol10.1099/ijs.0.02423-02003Enterobacteriaceae/*classification/genetics, Nucleic Acid Hybridization, *Phylogeny, Plant Diseases/microbiology, RNA, Ribosomal, 16S/analysis, Species Specificity
Genetics25297844Genomic overview of the phytopathogen Pectobacterium wasabiae strain RNS 08.42.1A suggests horizontal acquisition of quorum-sensing genes.Khayi S, Raoul des Essarts Y, Quetu-Laurent A, Moumni M, Helias V, Faure DGenetica10.1007/s10709-014-9793-22014DNA, Bacterial/genetics, *Gene Transfer, Horizontal, *Genome, Bacterial, Molecular Sequence Data, Pectobacterium/*genetics/isolation & purification/pathogenicity, Phylogeny, Plant Diseases/microbiology, Quorum Sensing/*genetics, Sequence Analysis, DNA, Solanum tuberosum/microbiology, Synteny, Virulence/geneticsPhylogeny
Phylogeny27692046Transfer of the potato plant isolates of Pectobacterium wasabiae to Pectobacterium parmentieri sp. nov.Khayi S, Cigna J, Chong TM, Quetu-Laurent A, Chan KG, Helias V, Faure DInt J Syst Evol Microbiol10.1099/ijsem.0.0015242016Bacterial Typing Techniques, DNA, Bacterial/genetics, Genes, Bacterial, Nucleic Acid Hybridization, Pectobacterium/*classification, *Phylogeny, Plant Diseases/*microbiology, Solanum tuberosum/*microbiology
Phylogeny30239330Pectobacterium punjabense sp. nov., isolated from blackleg symptoms of potato plants in Pakistan.Sarfraz S, Riaz K, Oulghazi S, Cigna J, Sahi ST, Khan SH, Faure DInt J Syst Evol Microbiol10.1099/ijsem.0.0030292018Bacterial Typing Techniques, DNA, Bacterial/genetics, Genes, Bacterial, Multilocus Sequence Typing, Nucleic Acid Hybridization, Pakistan, Pectobacterium/*classification/genetics/isolation & purification, *Phylogeny, Plant Diseases/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Solanum tuberosum/*microbiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7375Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18074)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18074
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
39223Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17186
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
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
74520Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID41768.1StrainInfo: A central database for resolving microbial strain identifiers
123913Curators of the CIPCollection of Institut Pasteur (CIP 105194)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105194