Strain identifier

BacDive ID: 5097

Type strain: Yes

Species: Klebsiella planticola

Strain Designation: CRCC 13986, V-236, 4245-72

Strain history: CIP <- 1984, ATCC <- R.J. Seider: strain V-236 <- CDC: strain 4245-72

NCBI tax ID(s): 1005996 (strain), 575 (species)

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General

@ref: 1288

BacDive-ID: 5097

DSM-Number: 3069

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, human pathogen

description: Klebsiella planticola CRCC 13986 is a facultative anaerobe, mesophilic, Gram-negative human pathogen that was isolated from radishroot.

NCBI tax id

NCBI tax idMatching level
1005996strain
575species

strain history

@refhistory
1288<- ATCC <- R.J. Seiler, V-236 <- C. Brown
67770ATCC 33531 <-- R. J. Seidler V-236 <-- C. Brown.
121867CIP <- 1984, ATCC <- R.J. Seider: strain V-236 <- CDC: strain 4245-72

doi: 10.13145/bacdive5097.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Enterobacteriaceae
  • genus: Klebsiella
  • species: Klebsiella planticola
  • full scientific name: Klebsiella planticola Bagley et al. 1982

  • synonyms

    @refsynonym
    20215Raoultella planticola
    20215Klebsiella trevisanii

@ref: 1288

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Raoultella

species: Raoultella planticola

full scientific name: Raoultella planticola (Bagley et al. 1982) Drancourt et al. 2001

strain designation: CRCC 13986, V-236, 4245-72

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.96
121867negativeoval-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1288NUTRIENT 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
38087MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121867CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
1288positivegrowth30mesophilic
38087positivegrowth30mesophilic
67770positivegrowth37mesophilic
121867positivegrowth5-41

Physiology and metabolism

oxygen tolerance

  • @ref: 121867
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.793

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-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
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
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
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
121867mannitol+fermentation29864
121867citrate+carbon source16947
121867glucose+fermentation17234
121867lactose+fermentation17716
121867nitrate+reduction17632
121867nitrite+reduction16301
121867malonate+assimilation15792
121867sodium thiosulfate-builds gas from132112
121867glucose+degradation17234

antibiotic resistance

  • @ref: 121867
  • 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
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12186735581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12186715688acetoin+
12186717234glucose+

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
68368beta-galactosidase+3.2.1.23
121867oxidase-
121867beta-galactosidase+3.2.1.23
121867alcohol dehydrogenase-1.1.1.1
121867gelatinase-
121867catalase+1.11.1.6
121867lysine decarboxylase+4.1.1.18
121867ornithine decarboxylase-4.1.1.17
121867phenylalanine ammonia-lyase-4.3.1.24
121867tryptophan deaminase-
121867urease+3.5.1.5

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOXNO2N2
1288+++-+-+--+-+++++++++-
1288+-+-+-+--+-+++++++++-+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121867+-+/-+++-+-++++++-+++-+++/-+/-++++++++--++/---+----++-+/-+/-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121867++++++++++++++++++++++--+-+----++++-++---+++---++++--+++++-++++++--+-+--++++---++-----+-+++++++----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
1288radishroot
46331Radish root
67770Radish root
121867Environment, Radish rootOregonUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
1288yes, in single casesyes, in single cases1Risk group (German classification)
1218672Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Klebsiella planticola strain ATCC 33531T 16S ribosomal RNA gene, partial sequenceAF1294431436ena1005996
20218Raoultella planticola strain ATCC 33531 16S ribosomal RNA gene, partial sequenceFJ971885795ena1005996
20218Klebsiella planticola 16S rRNA gene, strain ATCC33531T, partialY176591452ena1005996
20218K.planticola 16S rRNA gene (strain DSM 3069 T)X932151401ena1005996
20218Vibrio diazotrophicus DNA, 16S-23S rRNA intergenic spacer type 1 and 23S rRNA, partial sequence, strain: IAM 14202AB255715305ena685
20218Vibrio diazotrophicus DNA, 16S-23S rRNA intergenic spacer type 2 and 23S rRNA, partial sequence, strain: IAM 14202AB255716292ena685
20218Vibrio diazotrophicus DNA, 16S-23S rRNA intergenic spacer type 3 and 23S rRNA, partial sequence, strain: IAM 14202AB255717285ena685
20218Vibrio diazotrophicus DNA, 16S-23S rRNA intergenic spacer type 4 and 23S rRNA, partial sequence, strain: IAM 14202AB255718290ena685
20218Raoultella planticola gene for 16S ribosomal RNA, partial sequenceAB0047551451ena1005996
20218Raoultella ornithinolytica gene for 16S ribosomal RNA, partial sequenceAB0047561441ena54291
20218Raoultella planticola gene for 16S rRNA, partial sequence, strain: NBRC 14939AB6807121465ena575

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Raoultella planticola ATCC 335311005996.3wgspatric1005996
66792Raoultella planticola strain NCTC12998575.52wgspatric575
66792Raoultella planticola ATCC 335312588253798draftimg1005996
67770Raoultella planticola ATCC 33531GCA_000735435contigncbi1005996
66792Raoultella planticola NCTC12998GCA_900706865contigncbi575

GC content

@refGC-contentmethod
128853.9
6777053.9thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno77.617no
flagellatedno93.733no
gram-positiveno97.235no
anaerobicno97.66no
aerobicyes90.239no
halophileno88.913no
spore-formingno94.756no
thermophileno99.511no
glucose-utilyes95.029no
glucose-fermentyes91.132no

External links

@ref: 1288

culture collection no.: CCUG 15718, DSM 3069, ATCC 33531, CDC 4245-72, IAM 14202, IFO 14939, JCM 7251, NBRC 14939, BCRC 13986, CECT 843, CIP 100751, NCIMB 11885, NCTC 12998, VTT E-981077, CRBIP28.102

straininfo link

  • @ref: 74591
  • straininfo: 92271

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism9281820Formate and ethanol are the major products of glycerol fermentation produced by a Klebsiella planticola strain isolated from red deer.Jarvis GN, Moore ER, Thiele JHJ Appl Microbiol10.1046/j.1365-2672.1997.00217.x1997Animals, Central Nervous System Depressants/metabolism, Deer/*microbiology, Ethanol/metabolism, Fermentation/*physiology, Formates/metabolism, Genes, Bacterial/genetics, Glycerol/*metabolism, Hemostatics/metabolism, Klebsiella/genetics/*metabolism/ultrastructure, Microscopy, Electron, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/isolation & purification, Rumen/microbiologyPhylogeny
Enzymology14693555Genetic and biochemical characterization of the chromosomal class A beta-lactamases of Raoultella (formerly Klebsiella) planticola and Raoultella ornithinolytica.Walckenaer E, Poirel L, Leflon-Guibout V, Nordmann P, Nicolas-Chanoine MHAntimicrob Agents Chemother10.1128/AAC.48.1.305-312.20042004Amino Acid Sequence, Anti-Bacterial Agents/pharmacology, Cloning, Molecular, DNA, Bacterial/genetics, Enterobacteriaceae/*genetics, Isoelectric Focusing, Microbial Sensitivity Tests, Molecular Sequence Data, Plasmids/genetics, beta-Lactamases/*genetics/isolation & purification/*metabolism, beta-Lactams/pharmacologyGenetics
16347427Fermentation of d-Xylose to Ethanol by Genetically Modified Klebsiella planticola.Tolan JS, Finn RKAppl Environ Microbiol10.1128/aem.53.9.2039-2044.19871987
Metabolism22395910Isolation and lipid degradation profile of Raoultella planticola strain 232-2 capable of efficiently catabolizing edible oils under acidic conditions.Sugimori D, Watanabe M, Utsue TAppl Microbiol Biotechnol10.1007/s00253-012-3982-72012Enterobacteriaceae/*isolation & purification/*metabolism, Hydrogen-Ion Concentration, Lipase/metabolism, Plant Oils/metabolism, Temperature, Triglycerides/metabolism, Water PurificationPhylogeny
Enzymology28515389Ca(2+) in Hybridization Solutions for Fluorescence in situ Hybridization Facilitates the Detection of Enterobacteriaceae.Haruta S, Iino T, Ohkuma M, Suzuki KI, Igarashi YMicrobes Environ10.1264/jsme2.ME161862017Calcium/*chemistry, Enterobacteriaceae/*isolation & purification, *In Situ Hybridization, Fluorescence, Oligonucleotide ProbesPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1288Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3069)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3069
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
38087Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/12250
46331Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 15718)https://www.ccug.se/strain?id=15718
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
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
74591Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92271.1StrainInfo: A central database for resolving microbial strain identifiers
121867Curators of the CIPCollection of Institut Pasteur (CIP 100751)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20100751