Paraburkholderia eburnea (DSM 29414, JCM 18070, KEMC 7302-065)

Name: Paraburkholderia eburnea (DSM 29414, JCM 18070, KEMC 7302-065)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130230

Type strain

Strain Designation RR11

Culture col. no. DSM 29414 JCM 18070 KEMC 7302-065 RR11 LMG 29537

NCBI tax ID(s) 1189126

Special Collections DSMZ JCM

History <- JCM <- S.-S. Lee; RR11 S.-S. Lee RR11.

Links

Paraburkholderia eburnea RR11 is a bacterium that was isolated from peat soil near coal mine.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 399001

LMG 29537,JCM 18070,DSM 29414

@ref 20215

Last LPSN update 2026-02-09 11:31:10

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Burkholderiaceae

Genus Paraburkholderia

Species Paraburkholderia eburnea

Full scientific name Paraburkholderia eburnea corrig. (Kang et al. 2014) Sawana et al. 2015

Synonyms (2)

Paraburkholderia eburne
Burkholderia eburnea

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	96.5
125439	negative	97.9

Colony morphology

21541

Incubation period1-2 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21541	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
21541	positive	growth	30
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.9

Spore formation

@ref	Spore formation	Confidence
125439		95.9

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
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	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
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	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

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

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
21541	catalase	+	1.11.1.6
21541	cytochrome-c oxidase	+	1.9.3.1
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	gallate degradation	100	5 of 5
66794	ribulose monophosphate pathway	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	pentose phosphate pathway	100	11 of 11
66794	threonine metabolism	100	10 of 10
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	Entner Doudoroff pathway	100	10 of 10
66794	butanoate fermentation	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	adipate degradation	100	2 of 2
66794	ethanol fermentation	100	2 of 2
66794	resorcinol degradation	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	starch degradation	100	10 of 10
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	taurine degradation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	quinate degradation	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	ubiquinone biosynthesis	100	7 of 7
66794	biotin biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	acetate fermentation	100	4 of 4
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	propionate fermentation	90	9 of 10
66794	phenol degradation	90	18 of 20
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	4-hydroxymandelate degradation	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	3-phenylpropionate degradation	86.67	13 of 15
66794	alanine metabolism	86.21	25 of 29
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	citric acid cycle	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	propanol degradation	85.71	6 of 7
66794	vitamin B12 metabolism	85.29	29 of 34
66794	methionine metabolism	84.62	22 of 26
66794	vitamin B1 metabolism	84.62	11 of 13
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	vitamin B6 metabolism	81.82	9 of 11
66794	tryptophan metabolism	81.58	31 of 38
66794	cellulose degradation	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	myo-inositol biosynthesis	80	8 of 10
66794	3-chlorocatechol degradation	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	4-hydroxyphenylacetate degradation	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	purine metabolism	78.72	74 of 94
66794	degradation of pentoses	78.57	22 of 28
66794	tyrosine metabolism	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	lysine metabolism	76.19	32 of 42
66794	degradation of sugar acids	76	19 of 25
66794	arginine metabolism	75	18 of 24
66794	glycogen biosynthesis	75	3 of 4
66794	degradation of sugar alcohols	75	12 of 16
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	non-pathway related	73.68	28 of 38
66794	pyrimidine metabolism	73.33	33 of 45
66794	proline metabolism	72.73	8 of 11
66794	d-xylose degradation	72.73	8 of 11
66794	cysteine metabolism	72.22	13 of 18
66794	glutathione metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	lipid metabolism	70.97	22 of 31
66794	urea cycle	69.23	9 of 13
66794	oxidative phosphorylation	69.23	63 of 91
66794	androgen and estrogen metabolism	68.75	11 of 16
66794	sulfoquinovose degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	flavin biosynthesis	66.67	10 of 15
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	metabolism of disaccharids	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	histidine metabolism	62.07	18 of 29
66794	sulfate reduction	61.54	8 of 13
66794	hydrogen production	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	polyamine pathway	56.52	13 of 23
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	cholesterol biosynthesis	54.55	6 of 11
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	sulfopterin metabolism	50	2 of 4
66794	pantothenate biosynthesis	50	3 of 6
66794	toluene degradation	50	2 of 4
66794	carnitine metabolism	50	4 of 8
66794	cyclohexanol degradation	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	catecholamine biosynthesis	50	2 of 4
66794	degradation of hexoses	50	9 of 18
66794	glycine metabolism	50	5 of 10
66794	coenzyme M biosynthesis	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	carotenoid biosynthesis	45.45	10 of 22
66794	nitrate assimilation	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	ascorbate metabolism	40.91	9 of 22
66794	vitamin K metabolism	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	chlorophyll metabolism	33.33	6 of 18
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	lactate fermentation	25	1 of 4
66794	ginsenoside metabolism	25	4 of 16
66794	methanogenesis from CO2	25	3 of 12
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	daunorubicin biosynthesis	22.22	2 of 9

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
21541	-	-	-	-	-	-	-	+	+	+/-	+	+	+	+/-	+	+	-	+	+	+	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Other	#Mine
#Environmental	#Terrestrial	#Soil
#Environmental	#Terrestrial	#Wetland (Swamp)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
21541	peat soil near coal mine	Prokopyevsk, Kemerovo Oblast	Russia	RUS	Asia	53.8808	86.7275 53.8808/86.7275
67770	Peat soil (pH 4.5) near a coal mine at Prokopyevsk	Kemerovo Oblast	Russia	RUS

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21541	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM300337v1 assembly for Paraburkholderia eburnea LMG 29537	scaffold	GCA_003003375	1189126.4	2708743144	1189126	68.15
67770	ASM291709v1 assembly for Paraburkholderia eburnea JCM 18070	scaffold	GCA_002917095	1189126.3	2708743145	1189126	67.76

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21541	Paraburkholderia eburnea strain RR11 from Russia 16S ribosomal RNA gene, partial sequence	JQ692176	1446		1189126

GC content

21541

GC-content (mol%)60.8

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paraburkholderia eburnea LMG 29537
NCBI: GCA_003003375

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.90	no
125439	gram_stain	BacteriaNetⓘ	negative	97.90	no
125439	motility	BacteriaNetⓘ	yes	63.90	no
125439	spore_formation	BacteriaNetⓘ	no	95.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paraburkholderia eburnea LMG 29537
NCBI: GCA_003003375.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.50	no
125438	anaerobic	anaerobicⓘ	no	95.82	no
125438	aerobic	aerobicⓘ	yes	88.45	no
125438	spore-forming	spore-formingⓘ	no	89.02	no
125438	thermophilic	thermophileⓘ	no	99.00	yes
125438	flagellated	motile2+ⓘ	yes	85.70	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Burkholderia eburnea sp. nov., isolated from peat soil.	Kang SR, Srinivasan S, Lee SS	Int J Syst Evol Microbiol	10.1099/ijs.0.051078-0	2013

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 )
#21541	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29414
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68369	Automatically annotated from API 20NE .
#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 )

Rate our new design

Content

About us

Paraburkholderia eburnea (DSM 29414, JCM 18070, KEMC 7302-065)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003003375

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media