Name: Klebsiella variicola LX3
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133650

Type strain:

Species: Klebsiella variicola

Strain Designation: LX3

Culture col. no.: DSM 16265, JCM 12419, CCUG 57108, CIP 108642, LMG 23571

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

NCBI tax ID(s): 2590157 (subspecies)

SI-ID 134436

DSM 16265, JCM 12419, CIP 108642, LMG 23571, CCUG 57108

Special Collections

Other strains from Klebsiella variicola

Section

When using BacDive for research please cite our paper

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Enterobacterales*
	Family	*Enterobacteriaceae*
	Genus	*Klebsiella*
	Species	**Klebsiella variicola**
	Full Scientific Name (LPSN)	Klebsiella variicola Rosenblueth et al. 2004

Synonym

Klebsiella singaporensis

Information on morphological and physiological properties Morphology

[Ref.: #29929]	Gram stain	negative
[Ref.: #123805]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %100
[Ref.: #125439]	Gram stain	negative Confidence in %97.1

[Ref.: #29929]	Cell length	1.45 µm

[Ref.: #29929]	Cell width	0.7 µm

[Ref.: #29929]	Cell shape	rod-shaped
[Ref.: #123805]	Cell shape	oval-shaped

[Ref.: #29929]	Motility	no
[Ref.: #123805]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #123805]

Culture medium

CIP Medium 72

[Ref.: #123805]

Culture medium growth

[Ref.: #123805]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #124891]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #124891]

Culture medium growth

[Ref.: #124891]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #124891]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #124891]

Culture medium growth

[Ref.: #124891]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #29929]		optimum	30 °C
[Ref.: #61197]		growth	30 °C
[Ref.: #67770]		growth	30 °C
[Ref.: #123805]		growth	10-41 °C
[Ref.: #123805]	negative	growth	5 °C
[Ref.: #124891]		growth	30 °C

	pH	Kind of pH		pH
[Ref.: #29929]			optimum	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29929]	Oxygen tolerance	facultative anaerobe
[Ref.: #61197]	Oxygen tolerance	aerobe
[Ref.: #123805]	Oxygen tolerance	facultative anaerobe

[Ref.: #29929]

Ability of spore formation

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29929]	citrate ChEBI	+	carbon source
[Ref.: #123805]	citrate ChEBI	+	carbon source
[Ref.: #29929]	glucose ChEBI	+	carbon source
[Ref.: #123805]	glucose ChEBI	+	fermentation
[Ref.: #123805]	lactose ChEBI	+	fermentation
[Ref.: #123805]	malonate ChEBI	+	assimilation
[Ref.: #123805]	mannitol ChEBI	+	fermentation
[Ref.: #123805]	nitrate ChEBI	+	reduction
[Ref.: #123805]	nitrite ChEBI	-	reduction
[Ref.: #123805]	sodium thiosulfate ChEBI	-	builds gas from

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #123805]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite production	Metabolite	Production
[Ref.: #29929]		indole ChEBI	yes
[Ref.: #123805]		indole ChEBI	no

	Metabolite	Voges-Proskauer-test	Methylred-test	Indole test
[Ref.: #123805]	acetoin ChEBI	+
[Ref.: #123805]	glucose ChEBI		-
[Ref.: #29929]	indole ChEBI			+

	Enzyme	Enzyme activity	EC number
[Ref.: #123805]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #123805]	beta-galactosidase	+	3.2.1.23
[Ref.: #29929]	catalase	+	1.11.1.6
[Ref.: #123805]	catalase	+	1.11.1.6
[Ref.: #123805]	gelatinase	-
[Ref.: #123805]	lysine decarboxylase	+	4.1.1.18
[Ref.: #123805]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #123805]	oxidase	-
[Ref.: #123805]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #123805]	tryptophan deaminase	-
[Ref.: #29929]	urease	+	3.5.1.5
[Ref.: #123805]	urease	+	3.5.1.5
	Only first 10 entries are displayed. Click here to see all.

API® Biotype100:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
[Ref.: #123805]	2849	not determinedn.d.	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	+	-	+	-	-	+	+	+	+	+	+	-	+	-	-	-	-	+	-	+	+	+	-	-	+	+	+	+	+	+	+	+	+	+	-	+	+	+	+	+	+	+	-	+	-	+	-	-	+	+	-	+	-	-	-	+	+	-	+	-	-	-	-	-	+	+	+	+	+	+	+	+	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #29929]	Sample type/isolated from	soil

[Ref.: #61197]	Sample type/isolated from	Soil of sugarcane field
[Ref.: #61197]	Country	Singapore
[Ref.: #61197]	Country ISO 3 Code	SGP
[Ref.: #61197]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil of sugarcane field

[Ref.: #123805]	Sample type/isolated from	Environment, Soil of sugarcane field
[Ref.: #123805]	Country	Singapore
[Ref.: #123805]	Country ISO 3 Code	SGP
[Ref.: #123805]	Continent	Asia

[Ref.: #124891]	Sample type/isolated from	soil samples (roots of sugarcane and Clementi Singapore)
[Ref.: #124891]	Country	Singapore
[Ref.: #124891]	Country ISO 3 Code	SGP
[Ref.: #124891]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC507453 (>99% sequence identity) for Klebsiella pneumoniae from Microbeatlas

Aquatic Samples	3887
Soil Samples	1141
Animal Samples	41102
Plant Samples	1362
Total Samples	47492

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #124891]	Pathogenicity (human)	yes
[Ref.: #124891]	Pathogenicity (animal)	yes
[Ref.: #124891]	Biosafety level	2	Risk group (German classification) According to TRBA 466
[Ref.: #123805]	Biosafety level	2	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Klebsiella variicola JCM 12419 gene for 16S ribosomal RNA, partial sequence	LC507453	1462	GenBank ENA	244366 tax ID
[Ref.: #29929]	Klebsiella singaporensis strain LX3 16S ribosomal RNA gene, partial sequence	AF250285	1282	GenBank ENA	244366 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Klebsiella variicola JCM 12419	GCA_018324045	complete	GenBank ENA	244366 tax ID	*
[Ref.: #66792]	Klebsiella variicola LMG 23571	GCA_001969305	complete	GenBank ENA	244366 tax ID	*
[Ref.: #66792]	Klebsiella variicola strain JCM 12419	244366.635	complete	PATRIC	244366 tax ID	*
[Ref.: #66792]	Klebsiella variicola strain LMG 23571	244366.305	complete	PATRIC	244366 tax ID	*
[Ref.: #66792]	Klebsiella variicola LMG 23571	2916621918	complete	JGI IMG/M	244366 tax ID	*

[Ref.: #29929]	GC-content	56.4 mol%
[Ref.: #67770]	GC-content	56.4 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Klebsiella variicola JCM 12419 NCBI: GCA_018324045.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	100	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	98.351	yes
[Ref.: #125438]	aerobic	aerobicⓘ	no	54.419	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	89.996	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	99	no
[Ref.: #125438]	motile2+	flagellatedⓘ	no	77.093	yes

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Klebsiella variicola JCM 12419 NCBI: GCA_018324045
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	87.6
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	74.7
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	97.1
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	aerobe	88.1

Availability in culture collections External links

[Ref.: #124891]

Culture collection no.

DSM 16265, JCM 12419, CCUG 57108, CIP 108642, LMG 23571

[Ref.: #91543]

SI-ID 134436

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Klebsiella singaporensis sp. nov., a novel isomaltulose-producing bacterium.	Li X, Zhang D, Chen F, Ma J, Dong Y, Zhang L	Int J Syst Evol Microbiol	10.1099/ijs.0.02690-0	2004	*

References

#20215

Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#29929

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #26300 (see below)

#61197 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 57108

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#69479

João 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 beta .

#91543

Reimer, 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 identifiers . ( DOI 10.60712/SI-ID134436.1 )

#123805 Collection of Institut Pasteur ; Curators of the CIP; CIP 108642

#124891

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16265

#125438

Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )

#125439

Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

#26300

IJSEM 2131 2004 ( DOI 10.1099/ijs.0.02690-0 , PubMed 15545446 )

* These data were automatically processed and therefore are not curated

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Klebsiella variicola JCM 12419

Klebsiella variicola JCM 12419

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