Strain identifier

BacDive ID: 4966

Type strain: Yes

Species: Klebsiella variicola

Strain Designation: F2R9

Strain history: CIP <- 2004, E. Martinez Romero, Mexico Univ., Cuernavaca, Morelos, Mexico: strain F2R9

NCBI tax ID(s): 244366 (species)

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General

@ref: 6208

BacDive-ID: 4966

DSM-Number: 15968

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped, human pathogen

description: Klebsiella variicola F2R9 is an aerobe, mesophilic, Gram-negative human pathogen that was isolated from banana root.

NCBI tax id

  • NCBI tax id: 244366
  • Matching level: species

strain history

@refhistory
6208<- E. Martínez-Romero; F2R9 <- L. Martinez
365942004, E. Martinez Romero, Mexico Univ., Cuernavaca, Morelos, Mexico: strain F2R9
123804CIP <- 2004, E. Martinez Romero, Mexico Univ., Cuernavaca, Morelos, Mexico: strain F2R9

doi: 10.13145/bacdive4966.20230509.8.1

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 variicola
  • full scientific name: Klebsiella variicola Rosenblueth et al. 2004

  • synonyms

    • @ref: 20215
    • synonym: Klebsiella singaporensis

@ref: 6208

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Enterobacteriaceae

genus: Klebsiella

species: Klebsiella variicola subsp. variicola

full scientific name: Klebsiella variicola subsp. variicola (Rosenblueth et al. 2004) Rodrigues et al. 2019

strain designation: F2R9

type strain: yes

Morphology

cell morphology

  • @ref: 123804
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6208NUTRIENT 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
36594MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
36595MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
6208TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
6208COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
123804CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
123804CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
6208positivegrowth30mesophilic
36594positivegrowth30mesophilic
36595positivegrowth30mesophilic
60074positivegrowth30-37mesophilic
123804positivegrowth10-41
123804nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
60074aerobe
123804facultative anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose+fermentation
6836827613amygdalin+fermentation
6836828053melibiose+fermentation
6836817992sucrose+fermentation
6836862345L-rhamnose+fermentation
6836830911sorbitol+fermentation
6836817268myo-inositol+fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816947citrate+assimilation
6836818257ornithine-degradation
6836829016arginine-hydrolysis
12380429864mannitol+fermentation
12380416947citrate+carbon source
1238044853esculin+hydrolysis
12380417234glucose+fermentation
12380417716lactose+fermentation
12380417632nitrate+reduction
12380416301nitrite+reduction
12380415792malonate+assimilation
123804132112sodium thiosulfate-builds gas from

antibiotic resistance

  • @ref: 123804
  • 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
12380435581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12380415688acetoin+
12380417234glucose-

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
68368ornithine decarboxylase-4.1.1.17
68368arginine dihydrolase-3.5.3.6
123804oxidase-
123804beta-galactosidase+3.2.1.23
123804alcohol dehydrogenase-1.1.1.1
123804gelatinase-
123804catalase+1.11.1.6
123804lysine decarboxylase+4.1.1.18
123804ornithine decarboxylase-4.1.1.17
123804phenylalanine ammonia-lyase-4.3.1.24
123804tryptophan deaminase-
123804urease-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
123804-+++-+----++++-++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
6208+---+-+--+-+++++++++-
6208--+-+----+-+++++++++-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123804++++++++++++++++-++++++++-+--++++++++----+-+++-++++++++++--+++++++-+-+--++-+--+++-++--+-++++++++---

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentlatitudelongitude
6208banana (Musa sp.) rootMusaColimaMexicoMEXNorth America19.0914-103.956
60074Banana root (Musa sp.)ColimaMexicoMEXNorth America
123804Plant, Banana rootMexicoMEXNorth America

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_10.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_7;98_9;99_10&stattab=map
  • Last taxonomy: Klebsiella pneumoniae
  • 16S sequence: NR_025635
  • Sequence Identity:
  • Total samples: 47492
  • soil counts: 1141
  • aquatic counts: 3887
  • animal counts: 41102
  • plant counts: 1362

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
6208yesyes2Risk group (German classification)
1238042Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Klebsiella variicola partial 16S rRNA geneAJ7839161412ena244366
6208Klebsiella variicola strain F2R9 16S ribosomal RNA, partial sequenceNR_0256351412nuccore244366

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Klebsiella variicola DSM 15968GCA_000828055completencbi244366
66792Klebsiella variicola F2R9GCA_017638945completencbi244366
66792Klebsiella variicola DSM 15968GCA_020115545contigncbi244366
66792Klebsiella variicola DSM 15968244366.17completepatric244366
66792Klebsiella variicola strain DSM 15968244366.674wgspatric244366
66792Klebsiella variicola DSM 159682630968774completeimg244366

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno83.913no
motileno83.913no
flagellatedno93.964no
flagellatedno93.964no
gram-positiveno97.265no
gram-positiveno97.265no
anaerobicno96.893yes
anaerobicno96.893yes
aerobicyes84.83no
aerobicyes84.83no
halophileno86.611no
halophileno86.611no
spore-formingno93.469no
spore-formingno93.469no
glucose-utilyes94.992no
glucose-utilyes94.992no
thermophileno99.657yes
thermophileno99.657yes
glucose-fermentyes91.133yes
glucose-fermentyes91.133yes

External links

@ref: 6208

culture collection no.: DSM 15968, ATCC BAA 830, CFNE 2004, CCUG 53906, CIP 108585

straininfo link

  • @ref: 74462
  • straininfo: 132018

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15053318Klebsiella variicola, a novel species with clinical and plant-associated isolates.Rosenblueth M, Martinez L, Silva J, Martinez-Romero ESyst Appl Microbiol10.1078/0723-2020-002612004Base Sequence, DNA, Bacterial/chemistry/genetics, Humans, Klebsiella/*classification/genetics/isolation & purification, Molecular Sequence Data, Musa/*microbiology, Nitrogen Fixation, Nucleic Acid Hybridization, Phylogeny, Polymerase Chain Reaction, Sequence AlignmentPathogenicity
Metabolism26471769Genomic identification of nitrogen-fixing Klebsiella variicola, K. pneumoniae and K. quasipneumoniae.Chen M, Li Y, Li S, Tang L, Zheng J, An QJ Basic Microbiol10.1002/jobm.2015004152015Bacterial Proteins/genetics, Base Sequence, Chromosome Mapping, DNA, Bacterial/genetics, *Genome, Bacterial, Gluconates/metabolism, Klebsiella/*genetics/*metabolism, Klebsiella pneumoniae/genetics/metabolism, Nitrogen/metabolism, *Nitrogen Fixation, Nitrogenase/genetics/metabolism, Operon, Oxidoreductases/genetics, Phylogeny, Polymerase Chain Reaction, Sequence Analysis, DNAGenetics
Genetics32675179Draft Genome Sequences of Plant-Pathogenic Klebsiella variicola Strains Isolated from Plantain in Haiti.Fulton JC, Klein JM, Bec S, Fayette J, Garrett KA, Jones JB, Timilsina S, Harmon CLMicrobiol Resour Announc10.1128/MRA.00336-202020Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6208Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15968)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15968
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
36594Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6230
36595Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6293
60074Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53906)https://www.ccug.se/strain?id=53906
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
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
74462Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132018.1StrainInfo: A central database for resolving microbial strain identifiers
123804Curators of the CIPCollection of Institut Pasteur (CIP 108585)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108585