Burkholderia ubonensis (DSM 17311, CCUG 48852, CIP 107078)

Name: Burkholderia ubonensis (DSM 17311, CCUG 48852, CIP 107078)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1964

Type strain

Strain Designation EY 3383

Culture col. no. DSM 17311 CCUG 48852 CIP 107078 NCTC 13147 LMG 20358 1 more

NCBI tax ID(s) 101571

Special Collections DSMZ CCUG CIP

History <- CCUG <- CIP <- E. Yabuuchi, GIFU; EY 3383 2001, E. Yabuuchi, Gifu University, Japan, strain: EY 3383 CIP <- 2001, E. Yabuuchi, Gifu Univ., Japan, strain: EY 3383

Links

Burkholderia ubonensis EY 3383 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from road-side surface soil.

Gram-negative motile rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 14631

LMG 20358,NCTC 13147,CIP 107078,CCUG 48852,DSM 17311

@ref 20215

Last LPSN update 2026-02-09 11:18:13

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Burkholderiaceae

Genus Burkholderia

Species Burkholderia ubonensis

Full scientific name Burkholderia ubonensis corrig. Yabuuchi et al. 2000

Synonyms (1)

Burkholderia uboniae

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
123706	negative	rod-shaped
125438	negative			98.302

Colony morphology

6890

Incubation period2-3 days

Pigmentation

@ref	Production	Name
123706		Pyocyanin

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6890	CASO AGAR (MERCK 105458) (DSMZ Medium 220)	Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
39650	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123706	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6890	positive	growth	30	mesophilic
39650	positive	growth	30	mesophilic
58360	positive	growth	30-37	mesophilic
123706	positive	growth	25-41
123706	negative	growth	5
123706	negative	growth	10

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
58360	aerobe
123706	obligate aerobe
125439	obligate aerobe	97.6

Spore formation

@ref	Spore formation	Confidence
125439		95.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
123706	NaCl	positive	growth	0-4 %
123706	NaCl		growth	6 %
123706	NaCl		growth	8 %
123706	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	+	assimilation	from API 20NE
68369	29016 ChEBI	arginine	+	hydrolysis	from API 20NE
123706	16947 ChEBI	citrate	+	carbon source
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	16899 ChEBI	D-mannitol	+	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	+	assimilation	from API 20NE
123706	4853 ChEBI	esculin	-	hydrolysis
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	+	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
123706	17632 ChEBI	nitrate	+	reduction
123706	17632 ChEBI	nitrate	-	respiration
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
123706	16301 ChEBI	nitrite	-	reduction
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
123706	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
123706	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
123706	alcohol dehydrogenase	+	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
123706	amylase	-
68369	arginine dihydrolase	+	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
123706	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
123706	caseinase	+	3.4.21.50
6890	catalase	+	1.11.1.6
123706	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
6890	cytochrome-c oxidase	+	1.9.3.1
123706	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
123706	gelatinase	+
68369	gelatinase	+		from API 20NE
123706	lecithinase	+
68382	leucine arylamidase	+	3.4.11.1	from API zym
123706	lipase	+
68382	lipase (C 14)	-		from API zym
123706	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
123706	ornithine decarboxylase	-	4.1.1.17
123706	oxidase	+
123706	protease	+
68382	trypsin	-	3.4.21.4	from API zym
123706	tryptophan deaminase	-
123706	tween esterase	+
123706	urease	+	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
123706	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	-	+	+	-	-

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
6890	+	-	+	+	-	-	+	-	+	+	+	+	+	+	+	+	+	+	+	+	+
6890	+	-	+/-	+	-	-	+	-	+	+	+	+	+	+	+	+	+	+	+	+	not determinedn.d.

API biotype100

@ref	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
123706	not determinedn.d.	+	+	+	+	+	-	-	+	+	+	+	-	-	-	-	+	+	-	+	+	+	+	+	-	+	-	+	-	-	-	-	+	+	+	+	+	+	-	-	-	-	+	-	+	+	+	-	-	+	+	+	+	-	+	+	+	+	+	-	+	+	+	+	+	+	-	-	+	-	-	-	+	+	+	-	+	+	+	-	+	+	-	-	+	+	-	+	-	+	+	+	+	+	+	-	-	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
6890	road-side surface soil		Ubon Ratchathani	Thailand	THA	Asia
58360	Soil,road-side surface soil	1989	Ubon Ratchatani	Thailand	THA	Asia
123706	Environment, Road-side, surface soil		Ubon Ratchatani	Thailand	THA	Asia	1989

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
6890	yes, in single cases	1	Risk group (German classification) According to TRBA 466
123706		1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM90283308v1 assembly for Burkholderia ubonensis LMG 20358	scaffold	GCA_902833085	101571.351	8115090965	101571	70.12
66792	ASM90249918v1 assembly for Burkholderia ubonensis	contig	GCA_902499185	101571.350	8115067496	101571	48.42

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Burkholderia ubonensis strain CIP 107078 16S ribosomal RNA gene, partial sequence	EU024179	1313	101571
6890	Burkholderia uboniae gene for 16S rRNA, partial sequence	AB030584	1388	101571
124043	Paenibacillus polymyxa strain LSU1 16S ribosomal RNA gene, partial sequence.	MT672505	1502	101571
124043	Burkholderia ubonensis strain CIP 107078 16S ribosomal RNA gene, partial sequence.	MT940989	1070	101571
124043	Burkholderia ubonensis strain CIP 107078 16S ribosomal RNA gene, partial sequence.	KX394776	879	101571

GC content

@ref	GC-content (mol%)	Method
6890	69.7	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Burkholderia ubonensis LMG 20358
NCBI: GCA_902833085

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.60	no
125439	gram_stain	BacteriaNetⓘ	negative	89.80	no
125439	motility	BacteriaNetⓘ	yes	68.90	no
125439	spore_formation	BacteriaNetⓘ	no	95.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Burkholderia ubonensis LMG 20358
NCBI: GCA_902833085.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.30	no
125438	anaerobic	anaerobicⓘ	no	97.65	yes
125438	aerobic	aerobicⓘ	yes	88.75	yes
125438	spore-forming	spore-formingⓘ	no	85.25	no
125438	thermophilic	thermophileⓘ	no	96.98	yes
125438	flagellated	motile2+ⓘ	yes	83.67	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Genomic Assemblies of Members of Burkholderia and Related Genera as a Resource for Natural Product Discovery.	Mullins AJ, Jones C, Bull MJ, Webster G, Parkhill J, Connor TR, Murray JAH, Challis GL, Mahenthiralingam E.	Microbiol Resour Announc	10.1128/mra.00485-20	2020
	Effect of beta-Lactamase inhibitors on in vitro activity of beta-Lactam antibiotics against Burkholderia cepacia complex species.	Everaert A, Coenye T.	Antimicrob Resist Infect Control	10.1186/s13756-016-0142-3	2016
Pathogenicity	Antibacterial activity of a lectin-like Burkholderia cenocepacia protein.	Ghequire MG, De Canck E, Wattiau P, Van Winge I, Loris R, Coenye T, De Mot R.	Microbiologyopen	10.1002/mbo3.95	2013
Pathogenicity	Investigating the Role of the Host Multidrug Resistance Associated Protein Transporter Family in Burkholderia cepacia Complex Pathogenicity Using a Caenorhabditis elegans Infection Model.	Tedesco P, Visone M, Parrilli E, Tutino ML, Perrin E, Maida I, Fani R, Ballestriero F, Santos R, Pinilla C, Di Schiavi E, Tegos G, de Pascale D.	PLoS One	10.1371/journal.pone.0142883	2015
Phylogeny	Burkholderia uboniae sp. nov., L-arabinose-assimilating but different from Burkholderia thailandensis and Burkholderia vietnamiensis.	Yabuuchi E, Kawamura Y, Ezaki T, Ikedo M, Dejsirilert S, Fujiwara N, Naka T, Kobayashi K	Microbiol Immunol	10.1111/j.1348-0421.2000.tb02500.x	2000

References

#6890	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17311
#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 )
#39650	; Curators of the CIP;
#58360	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 48852
#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) .
#68369	Automatically annotated from API 20NE .
#68382	Automatically annotated from API zym .
#123706	Collection of Institut Pasteur ; Curators of the CIP; CIP 107078
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Burkholderia ubonensis (DSM 17311, CCUG 48852, CIP 107078)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_902833085

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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