Strain identifier

BacDive ID: 5002

Type strain: Yes

Species: Pantoea cypripedii

Strain Designation: 4778

Strain history: CIP <- 1997, CFPB <- M.P. Starr <- P. Ark: strain 4778

NCBI tax ID(s): 55209 (species)

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General

@ref: 1493

BacDive-ID: 5002

DSM-Number: 3873

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

description: Pantoea cypripedii 4778 is a facultative anaerobe, mesophilic, motile plant pathogen that was isolated from cypripedium orchid.

NCBI tax id

  • NCBI tax id: 55209
  • Matching level: species

strain history

@refhistory
1493<- PDDCC
118832CIP <- 1997, CFPB <- M.P. Starr <- P. Ark: strain 4778

doi: 10.13145/bacdive5002.20230509.8.1

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 cypripedii
  • full scientific name: Pantoea cypripedii (Hori 1911) Brady et al. 2010

  • synonyms

    @refsynonym
    20215Bacillus cypripedii
    20215Pectobacterium cypripedii
    20215Erwinia cypripedii

@ref: 1493

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Erwiniaceae

genus: Pantoea

species: Pantoea cypripedii

full scientific name: Pantoea cypripedii (Hori 1911) Brady et al. 2010

strain designation: 4778

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.937
6948099.987negative
118832yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1493NUTRIENT 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
1493GLUCOSE YEAST EXTRACT MEDIUM (DSMZ Medium 54)yeshttps://mediadive.dsmz.de/medium/54Name: GLUCOSE YEAST EXTRACT MEDIUM (DSMZ Medium 54) Composition: CaCO3 20.0 g/l Glucose 20.0 g/l Agar 17.0 g/l Yeast extract 10.0 g/l Distilled water
39225MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118832CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
1493positivegrowth26mesophilic
39225positivegrowth30mesophilic
118832positivegrowth25-37mesophilic
118832nogrowth5psychrophilic
118832nogrowth10psychrophilic
118832nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118832
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.639

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
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
68371lactose-builds acid from17716
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
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
118832mannitol+fermentation29864
118832citrate+carbon source16947
118832glucose+fermentation17234
118832lactose-fermentation17716
118832nitrate+reduction17632
118832nitrite-reduction16301
118832malonate+assimilation15792
118832sodium thiosulfate-builds gas from132112
118832glucose+degradation17234

antibiotic resistance

  • @ref: 118832
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
11883235581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
11883215688acetoin-
11883217234glucose+

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
118832oxidase-
118832beta-galactosidase+3.2.1.23
118832alcohol dehydrogenase-1.1.1.1
118832gelatinase-
118832catalase+1.11.1.6
118832lysine decarboxylase-4.1.1.18
118832ornithine decarboxylase-4.1.1.17
118832phenylalanine ammonia-lyase+4.3.1.24
118832tryptophan deaminase-
118832urease-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
118832-++--+----++-+--++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
1493+---+------+++++++++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118832+--+++---++++-+-++---+-+++++/--+/-++----------+/-+/---+-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118832+++++--+-++----+-+++++-+-------+++-----+---++++++++--+++++-++---+--------+-+--+++-+---+--++-+++----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
1493cypripedium orchidCaliforniaUSAUSANorth America
118832Brown spot and rot of lady-slipper orchid, Cyprypedium sp.Berkeley, CaliforniaUnited States of AmericaUSANorth America

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_6218.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_310;97_344;98_389;99_6218&stattab=map
  • Last taxonomy: Pantoea
  • 16S sequence: U80201
  • Sequence Identity:
  • Total samples: 819
  • soil counts: 33
  • aquatic counts: 44
  • animal counts: 591
  • plant counts: 151

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
1493yes1Risk group (German classification)
1188321Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pantoea cypripedii strain LMG 2657 16S ribosomal RNA gene, partial sequenceJQ7111451500ena55209
20218Erwinia cypripedii 16S ribosomal RNA gene, partial sequenceU802011457ena55209
20218Erwinia cyrpipedii LMG 2657 16S ribosomal RNAZ960941485ena55209
1493Erwinia cypripedii 16S rRNA gene (strain DSM 3873)AJ2334131495ena55209

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pantoea cypripedii LMG 2657GCA_002095535contigncbi55209
66792Pantoea cypripedii strain LMG 265755209.3wgspatric55209
66792Pantoea cypripedii LMG 26572791355165draftimg55209

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.254no
anaerobicno97.516no
halophileno88.547no
spore-formingno94.688no
glucose-utilyes95.267no
thermophileno99.296yes
aerobicno63.167no
motileyes88.43no
flagellatedno73.025no
glucose-fermentyes89.102yes

External links

@ref: 1493

culture collection no.: DSM 3873, ATCC 29267, LMG 2655, LMG 2657, PDDCC 1591-66, CIP 105195, NCPPB 3004, CFPB 3613, PDDCC 1591, ICPB EC 155

straininfo link

  • @ref: 74497
  • straininfo: 2650

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology9352901Cloning and expression of a gene cluster encoding three subunits of membrane-bound gluconate dehydrogenase from Erwinia cypripedii ATCC 29267 in Escherichia coli.Yum DY, Lee YP, Pan JGJ Bacteriol10.1128/jb.179.21.6566-6572.19971997Amino Acid Sequence, Apoenzymes/genetics, Base Sequence, Carbohydrate Dehydrogenases/*genetics, Cloning, Molecular, Erwinia/enzymology/*genetics, Escherichia coli/genetics, *Genes, Bacterial, Gluconates/metabolism, Glucose/metabolism, Membrane Proteins/*genetics, Molecular Sequence Data, *Multigene Family, PQQ Cofactor, Quinolones, Quinones, Restriction Mapping, Sequence Analysis, DNA, Sequence Homology, Amino AcidMetabolism
Phylogeny19946052Emended 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.Brady CL, Cleenwerck I, Venter SN, Engelbeen K, De Vos P, Coutinho TAInt J Syst Evol Microbiol10.1099/ijs.0.017301-02009Bacterial 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, DNAPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1493Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3873)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3873
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
39225Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17187
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)
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
74497Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2650.1StrainInfo: A central database for resolving microbial strain identifiers
118832Curators of the CIPCollection of Institut Pasteur (CIP 105195)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105195