Strain identifier

BacDive ID: 5026

Type strain: Yes

Species: Pectobacterium betavasculorum

Strain Designation: UCPB 193

Strain history: CIP <- 1997, CFPB <- S.V. Thomson

NCBI tax ID(s): 55207 (species)

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General

@ref: 7377

BacDive-ID: 5026

DSM-Number: 18076

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

description: Pectobacterium betavasculorum UCPB 193 is a facultative anaerobe, mesophilic, motile plant pathogen that was isolated from Beta vulgaris cv. Saccharata.

NCBI tax id

  • NCBI tax id: 55207
  • Matching level: species

strain history

@refhistory
7377<- CFBP <- S. V. Thomson <- M. Schroth
116795CIP <- 1997, CFPB <- S.V. Thomson

doi: 10.13145/bacdive5026.20230509.8.1

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 betavasculorum
  • full scientific name: Pectobacterium betavasculorum (Thomson et al. 1984) Gardan et al. 2003

  • synonyms

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

@ref: 7377

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Pectobacteriaceae

genus: Pectobacterium

species: Pectobacterium betavasculorum

full scientific name: Pectobacterium betavasculorum (Thomson et al. 1984) Gardan et al. 2003

strain designation: UCPB 193

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.979
6948099.981negative
116795yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7377TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
41562MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
116795CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
7377positivegrowth30mesophilic
41562positivegrowth25mesophilic
116795positivegrowth10-37
116795nogrowth5psychrophilic
116795nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116795
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.925

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
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
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
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
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
68368nitrate+reduction17632
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
116795mannitol+fermentation29864
116795citrate-carbon source16947
116795esculin+hydrolysis4853
116795glucose+fermentation17234
116795lactose-fermentation17716
116795nitrate+reduction17632
116795nitrite-reduction16301
116795malonate-assimilation15792
116795sodium thiosulfate-builds gas from132112
116795glucose+degradation17234

antibiotic resistance

  • @ref: 116795
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836817997dinitrogenno
6836816301nitriteyes
6836835581indoleno
6836816136hydrogen sulfideno
11679535581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836835581indole-
11679515688acetoin+
11679517234glucose-

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
116795oxidase-
116795beta-galactosidase+3.2.1.23
116795alcohol dehydrogenase-1.1.1.1
116795gelatinase-
116795catalase+1.11.1.6
116795lysine decarboxylase-4.1.1.18
116795ornithine decarboxylase-4.1.1.17
116795phenylalanine ammonia-lyase-4.3.1.24
116795tryptophan deaminase-
116795urease-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
116795-+++-+--+-++---++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOXNO2N2
7377+--------+/--+++-++-++-+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116795+/---+++---++++-+-+/-+--+++/-+++----+---++/---+-------+/---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116795+++++--++-------++++++++-------+++-------+-++----+---------++--------------+----+-----+--+----+----

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
7377Beta vulgaris cv. SaccharataBeta vulgarisCalifornia, Kern countryUSAUSANorth America
116795Beta vulgarisUnited States of AmericaUSANorth America1971

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_7948.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_451;97_517;98_595;99_7948&stattab=map
  • Last taxonomy: Pectobacterium
  • 16S sequence: Z96091
  • Sequence Identity:
  • Total samples: 347
  • soil counts: 36
  • aquatic counts: 89
  • animal counts: 173
  • plant counts: 49

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
7377yes1Risk group (German classification)
1167951Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pectobacterium betavasculorum strain CFBP 2122 16S ribosomal RNA gene, partial sequenceJN6003281530ena55207
20218Pectobacterium betavasculorum strain CFBP 2122 16S ribosomal RNA gene, partial sequenceJN6003291530ena55207
20218Pectobacterium betavasculorum strain DSM 18076 16S ribosomal RNA gene, partial sequenceKJ7443111358ena55207
7377Erwinia carotovora LMG 2466 16S ribosomal RNAZ960911497ena554

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pectobacterium betavasculorum NCPPB 2795GCA_000749845contigncbi55207
66792Pectobacterium betavasculorum strain NCPPB 279555207.5wgspatric55207
66792Pectobacterium betavasculorum NCPPB 27952740892410draftimg55207

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno88no
gram-positiveno98.113no
anaerobicno97.738no
halophileno85.416no
spore-formingno94.68no
glucose-utilyes94.081no
thermophileno98.928yes
aerobicyes65.003no
motileyes91.435no
flagellatedyes64.432no
glucose-fermentyes88.317yes

External links

@ref: 7377

culture collection no.: DSM 18076, CFBP 2122, NCPPB 2795, CIP 105193, LMG 2464, ICMP 4226, CFPB 2122

straininfo link

  • @ref: 74521
  • straininfo: 2504

literature

  • topic: Phylogeny
  • Pubmed-ID: 12710602
  • title: Elevation of three subspecies of Pectobacterium carotovorum to species level: Pectobacterium atrosepticum sp. nov., Pectobacterium betavasculorum sp. nov. and Pectobacterium wasabiae sp. nov.
  • authors: Gardan L, Gouy C, Christen R, Samson R
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02423-0
  • year: 2003
  • mesh: Enterobacteriaceae/*classification/genetics, Nucleic Acid Hybridization, *Phylogeny, Plant Diseases/microbiology, RNA, Ribosomal, 16S/analysis, Species Specificity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7377Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18076)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18076
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
41562Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17185
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
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)
74521Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2504.1StrainInfo: A central database for resolving microbial strain identifiers
116795Curators of the CIPCollection of Institut Pasteur (CIP 105193)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105193