Strain identifier

BacDive ID: 133650

Type strain: No

Species: Klebsiella variicola

Strain Designation: LX3

Strain history: <- X. Li, College of Bio & Food Technology, Dalian Polytechnic University, P.R. China; LX3

NCBI tax ID(s): 2590157 (subspecies)

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General

@ref: 124891

BacDive-ID: 133650

DSM-Number: 16265

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, rod-shaped

description: Klebsiella variicola LX3 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 2590157
  • Matching level: subspecies

strain history

@refhistory
67770X. Li LX3.
123805CIP <- 2005, JCM, Klebsiella singaporensis <- 2004, X. Li: strain LX3
124891<- X. Li, College of Bio & Food Technology, Dalian Polytechnic University, P.R. China; LX3

doi: 10.13145/bacdive133650.20250331.9.3

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: 124891

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacterales

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: LX3

type strain: no

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29929negative1.45 µm0.7 µmrod-shapedno
125438negative100
125439negative97.1
123805negativeoval-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlink
123805CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
124891TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium92.pdf
124891COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium693.pdf

culture temp

@refgrowthtypetemperature
29929positiveoptimum30
61197positivegrowth30
67770positivegrowth30
123805positivegrowth10-41
123805nogrowth5
124891positivegrowth30

culture pH

  • @ref: 29929
  • ability: positive
  • type: optimum
  • pH: 7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29929facultative anaerobe
61197aerobe
123805facultative anaerobe

spore formation

  • @ref: 29929
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2992916947citrate+carbon source
2992917234glucose+carbon source
12380529864mannitol+fermentation
12380516947citrate+carbon source
12380517234glucose+fermentation
12380517716lactose+fermentation
12380517632nitrate+reduction
12380516301nitrite-reduction
12380515792malonate+assimilation
123805132112sodium thiosulfate-builds gas from

antibiotic resistance

  • @ref: 123805
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
2992935581indoleyes
12380535581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
2992935581indole+
12380515688acetoin+
12380517234glucose-

enzymes

@refvalueactivityec
29929catalase+1.11.1.6
29929urease+3.5.1.5
123805oxidase-
123805beta-galactosidase+3.2.1.23
123805alcohol dehydrogenase-1.1.1.1
123805gelatinase-
123805catalase+1.11.1.6
123805lysine decarboxylase+4.1.1.18
123805ornithine decarboxylase-4.1.1.17
123805phenylalanine ammonia-lyase-4.3.1.24
123805tryptophan deaminase-
123805urease+3.5.1.5

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123805+++++++++++++++++++++++++-+--++++++-+----+-+++--++++++++++-+++++++-+-+--++-+---++-+-----++++++++---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
29929soil
61197Soil of sugarcane fieldSingaporeSGPAsia
67770Soil of sugarcane field
123805Environment, Soil of sugarcane fieldSingaporeSGPAsia
124891soil samples (roots of sugarcane and Clementi Singapore)SingaporeSGPAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

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: LC507453
  • Sequence Identity:
  • Total samples: 47492
  • soil counts: 1141
  • aquatic counts: 3887
  • animal counts: 41102
  • plant counts: 1362

Safety information

risk assessment

@refbiosafety levelbiosafety level commentpathogenicity humanpathogenicity animal
1238052Risk group (French classification)
1248912Risk group (German classification)yesyes

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
29929Klebsiella singaporensis strain LX3 16S ribosomal RNA gene, partial sequenceAF2502851282nuccore244366
67770Klebsiella variicola JCM 12419 gene for 16S ribosomal RNA, partial sequenceLC5074531462nuccore244366

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Klebsiella variicola JCM 12419GCA_018324045completencbi244366
66792Klebsiella variicola LMG 23571GCA_001969305completencbi244366
66792Klebsiella variicola strain JCM 12419244366.635completepatric244366
66792Klebsiella variicola strain LMG 23571244366.305completepatric244366
66792Klebsiella variicola LMG 235712916621918completeimg244366

GC content

@refGC-contentmethod
2992956.4
6777056.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno100yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.351yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no54.419no
125438spore-formingspore-formingAbility to form endo- or exosporesno89.996yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno99no
125438motile2+flagellatedAbility to perform flagellated movementno77.093yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesno87.6
125439BacteriaNetmotilityAbility to perform movementyes74.7
125439BacteriaNetgram_stainReaction to gram-stainingnegative97.1
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe88.1

External links

@ref: 124891

culture collection no.: DSM 16265, JCM 12419, CCUG 57108, CIP 108642, LMG 23571

straininfo link

  • @ref: 91543
  • straininfo: 134436

literature

  • topic: Phylogeny
  • Pubmed-ID: 15545446
  • title: Klebsiella singaporensis sp. nov., a novel isomaltulose-producing bacterium.
  • authors: Li X, Zhang D, Chen F, Ma J, Dong Y, Zhang L
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02690-0
  • year: 2004
  • mesh: Anaerobiosis, Bacterial Capsules/biosynthesis, Base Composition, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, DNA-Directed RNA Polymerases/genetics, Genes, rRNA, Gentian Violet, Glucose/metabolism, Indoles/metabolism, Isomaltose/*analogs & derivatives/*biosynthesis, Klebsiella/*classification/cytology/*isolation & purification/physiology, Lactose/metabolism, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Phenazines, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial/cytology, Sucrose/metabolism, Temperature
  • topic2: Metabolism

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
29929Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172630028776041
61197Curators of the CCUGhttps://www.ccug.se/strain?id=57108Culture Collection University of Gothenburg (CCUG) (CCUG 57108)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
91543Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID134436.1
123805Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108642Collection of Institut Pasteur (CIP 108642)
124891Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-16265Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16265)
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG