Name: Klebsiella ornithinolytica DSM 7464
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 5102

Type strain:

Species: Klebsiella ornithinolytica

Culture col. no.: DSM 7464, CCM 4873, JCM 6096, NIH 90-72, ATCC 31898, CCUG 26769, CIP 103364, CIP 103576, NBRC 105727, CCUG 26625

Strain history: CIP <- 1989, JCM <- strain NIH 90-72

NCBI tax ID(s): 1349784 (strain), 54291 (species)

SI-ID 40240

ATCC 31898, CIP 103576, CCUG 26769, JCM 6096, CIP 103364, CCUG 26625, DSM 7464, CCM 4873, CCUG 26625 B

Special Collections

Section

Klebsiella ornithinolytica DSM 7464 is a Gram-negative bacterium that was isolated from urine.

Gram-negative
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Enterobacterales*
	Family	*Enterobacteriaceae*
	Genus	*Klebsiella*
	Species	**Klebsiella ornithinolytica**
	Full Scientific Name (LPSN)	Klebsiella ornithinolytica Sakazaki et al. 1989

Synonym

Raoultella ornithinolytica

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %98

Information on culture and growth conditions Culture and growth conditions

[Ref.: #3169]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

CASO AGAR (MERCK 105458) (DSMZ Medium 220)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

[Ref.: #35540]

Culture medium

MEDIUM 3 - Columbia agar

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Culture medium growth

[Ref.: #35540]

Culture medium composition

expand / minimize

[Ref.: #121449]

Culture medium

CIP Medium 72

[Ref.: #121449]

Culture medium growth

[Ref.: #121449]

Culture medium link

Medium recipe provided by DSMZ

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Culture medium

CIP Medium 3

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Culture medium growth

[Ref.: #121449]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #35569]

Culture medium

CIP Medium 3

[Ref.: #35569]

Culture medium growth

[Ref.: #35569]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #3169]	growth	30 °C
[Ref.: #35540]	growth	30 °C
[Ref.: #67770]	growth	37 °C

Information on physiology and metabolism Physiology and metabolism

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68368]	amygdalin ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	arginine ChEBI	-	hydrolysis	* from API 20E
[Ref.: #68368]	citrate ChEBI	+	assimilation	* from API 20E
[Ref.: #68368]	D-glucose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	D-mannitol ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	gelatin ChEBI	+	hydrolysis	* from API 20E
[Ref.: #68368]	L-arabinose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	L-rhamnose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	lysine ChEBI	+	degradation	* from API 20E
[Ref.: #68368]	melibiose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	myo-inositol ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	ornithine ChEBI	+	degradation	* from API 20E
[Ref.: #68368]	sorbitol ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	sucrose ChEBI	+	fermentation	* from API 20E
[Ref.: #68368]	tryptophan ChEBI	+	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	+	hydrolysis	* from API 20E
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #68368]	acetoin ChEBI	no	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68368]	indole ChEBI	yes	* from API 20E

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #68368]		acetoin ChEBI	-		* from API 20E
[Ref.: #68368]		indole ChEBI		+	* from API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #68368]	arginine dihydrolase	-	3.5.3.6	* from API 20E
[Ref.: #68368]	beta-galactosidase	+	3.2.1.23	* from API 20E
[Ref.: #68368]	cytochrome oxidase	+	1.9.3.1	* from API 20E
[Ref.: #68368]	gelatinase	+		* from API 20E
[Ref.: #68368]	lysine decarboxylase	+	4.1.1.18	* from API 20E
[Ref.: #68368]	ornithine decarboxylase	+	4.1.1.17	* from API 20E
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #68368]	urease	+	3.5.1.5	* from API 20E

API® 20E:

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

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #3169]	17783	+	-	+	+	+	-	+	-	+	-	+	+	+	+	+	+	+	+	+	+	+	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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

[Ref.: #3169]	Sample type/isolated from	urine
[Ref.: #3169]	Country	Japan
[Ref.: #3169]	Country ISO 3 Code	JPN
[Ref.: #3169]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Urine
* marker position based on {}

Isolation sources categories

#Host Body Product

#Fluids

#Urine

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence U78182 (>99% sequence identity) for Enterobacteriaceae from Microbeatlas

Aquatic Samples	20
Soil Samples	22
Animal Samples	107
Plant Samples	10
Total Samples	159

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

[Ref.: #3169]	Biosafety level	2	Risk group (German classification) According to TRBA 466
[Ref.: #121449]	Biosafety level	2	Risk group (French classification)

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

16S Sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #3169]	Klebsiella ornithinolytica partial 16S rRNA gene, strain JCM6096T	AJ251467	1516	GenBank ENA	54291 tax ID
[Ref.: #124043]	Raoultella ornithinolytica gene for 16S rRNA, partial sequence, strain: NBRC 105727.	AB682291	1465	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Klebsiella ornithinolytica strain ATCC 31898 16S ribosomal RNA gene, partial sequence	AF129441	1436	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Raoultella ornithinolytica culture-collection ATCC:31898 clone n17 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequence	EU623102	379	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Raoultella ornithinolytica culture-collection ATCC:31898 clone n18 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequence	EU623103	379	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Raoultella ornithinolytica culture-collection ATCC:31898 clone n19 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequence	EU623104	379	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Raoultella ornithinolytica culture-collection ATCC:31898 clone n20 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequence	EU623105	379	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Raoultella ornithinolytica culture-collection ATCC:31898 clone n21 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequence	EU623106	379	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Raoultella ornithinolytica culture-collection ATCC:31898 clone n22 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequence	EU623107	379	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Raoultella ornithinolytica culture-collection ATCC:31898 clone n23 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequence	EU623108	379	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Raoultella ornithinolytica culture-collection ATCC:31898 clone p13 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequence	EU623109	379	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Raoultella ornithinolytica culture-collection ATCC:31898 clone p14 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequence	EU623110	379	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Raoultella ornithinolytica culture-collection ATCC:31898 clone n16 16S-23S ribosomal RNA intergenic spacer, partial sequence	EU623111	233	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Raoultella ornithinolytica culture-collection ATCC:31898 clone p15 16S-23S ribosomal RNA intergenic spacer, partial sequence	EU623112	233	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Raoultella ornithinolytica culture-collection ATCC:31898 clone p16 16S-23S ribosomal RNA intergenic spacer, partial sequence	EU623113	233	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Raoultella ornithinolytica strain CCM4873 clone h02 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequence	EU623091	338	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Raoultella ornithinolytica strain CCM4873 clone h03 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequence	EU623092	379	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Raoultella ornithinolytica strain CCM4873 clone h06 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequence	EU623093	379	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Raoultella ornithinolytica strain CCM4873 clone h11 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequence	EU623094	379	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Raoultella ornithinolytica strain CCM4873 clone h12 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Glu gene, complete sequence	EU623095	379	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Raoultella ornithinolytica strain CCM4873 clone h04 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Ile and tRNA-Ala genes, complete sequence	EU623096	539	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Raoultella ornithinolytica strain CCM4873 clone h08 16S-23S ribosomal RNA intergenic spacer, partial sequence; and tRNA-Ile and tRNA-Ala genes, complete sequence	EU623097	539	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Raoultella ornithinolytica strain CCM4873 clone h01 16S-23S ribosomal RNA intergenic spacer, partial sequence	EU623098	232	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Raoultella ornithinolytica strain CCM4873 clone h05 16S-23S ribosomal RNA intergenic spacer, partial sequence	EU623099	232	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Raoultella ornithinolytica strain CCM4873 clone h07 16S-23S ribosomal RNA intergenic spacer, partial sequence	EU623100	232	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Raoultella ornithinolytica strain CCM4873 clone h10 16S-23S ribosomal RNA intergenic spacer, partial sequence	EU623101	232	GenBank ENA	54291 tax ID	*
[Ref.: #20218]	Raoultella ornithinolytica strain CIP 103364 16S ribosomal RNA gene, partial sequence	U78182	1502	GenBank ENA	54291 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Raoultella ornithinolytica NBRC 105727 = ATCC 31898	GCA_001598295	contig	GenBank ENA	1349784 tax ID

[Ref.: #3169]	GC-content	57.0 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #67770]	GC-content	57 mol%	thermal denaturation, midpoint method (Tm)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Raoultella ornithinolytica NBRC 105727 = ATCC 31898 NBRC 105727 NCBI: GCA_001598295.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.826	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	55.459	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	88.15	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	98.5	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	70.405	no

Availability in culture collections External links

[Ref.: #3169]

Culture collection no.

DSM 7464, CCM 4873, JCM 6096, NIH 90-72, ATCC 31898, CCUG 26769, CIP 103364, CIP 103576, NBRC 105727, CCUG 26625

[Ref.: #74596]

SI-ID 40240

Literature:

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Enhanced Bacterial Growth and Gene Expression of D-Amino Acid Dehydrogenase With D-Glutamate as the Sole Carbon Source.	Naganuma T, Iinuma Y, Nishiwaki H, Murase R, Masaki K, Nakai R	Front Microbiol	10.3389/fmicb.2018.02097	2018	*
Phylogeny	Benzoic acid-degrading bacteria from the intestinal tract of Macrotermes michaelseni Sjostedt.	Kamanda Ngugi D, Khamis Tsanuo M, Iddi Boga H	J Basic Microbiol	10.1002/jobm.200610142	2007	*
Enzymology	Genetic 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 MH	Antimicrob Agents Chemother	10.1128/AAC.48.1.305-312.2004	2004	*

References

#3169

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 7464

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#35540 ; Curators of the CIP;
#35569 Collection of Institut Pasteur ; Curators of the CIP; CIP 103576
#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68368

Automatically annotated from API 20E .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#74596

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-ID40240.1 )

#121449 Collection of Institut Pasteur ; Curators of the CIP; CIP 103364

#124043

Dr. Isabel Schober, Dr. Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

* These data were automatically processed and therefore are not curated

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Search for species Raoultella ornithinolytica in external resources:
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Raoultella ornithinolytica NBRC 105727 = ATCC 31898 NBRC 105727

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