Paraburkholderia megapolitana (DSM 23488, CCUG 53006, LMG 23650)

Name: Paraburkholderia megapolitana (DSM 23488, CCUG 53006, LMG 23650)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1979

Type strain

Strain Designation A3

Culture col. no. DSM 23488 CCUG 53006 LMG 23650 A3

NCBI tax ID(s) 420953

Special Collections DSMZ CCUG Literature strains

History <- CCUG <- G. Berg; A3

Links

Paraburkholderia megapolitana A3 is an aerobe, Gram-negative bacterium that was isolated from Aulacomnium palustre.

Gram-negative aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 137278

LMG 23650,CCUG 53006,DSM 23488

@ref 20215

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

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Burkholderiaceae

Genus Paraburkholderia

Species Paraburkholderia megapolitana

Full scientific name Paraburkholderia megapolitana (Vandamme et al. 2007) Sawana et al. 2015

Synonyms (1)

Burkholderia megapolitana

BacDive ID	Other strains from **Paraburkholderia megapolitana** (2)	Type strain
154306	P. megapolitana CCUG 53007
154307	P. megapolitana CCUG 53008, LMG 23652

Morphology

Cell morphology

@ref	Gram stain	Motility	Confidence
32217	negative
125438	negative		95.5

Colony morphology

@ref	Type of hemolysis	Incubation period
17236	gamma
59778		6 days

Pigmentation

32217

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17236	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)
32217	positive	optimum	28
59778	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
59778	aerobe
125438	aerobe	90.391
125439	obligate aerobe	98.5

Spore formation

32217

Spore formationno

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32217	22599 ChEBI	arabinose	+	carbon source
32217	29016 ChEBI	arginine	+	carbon source
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
32217	27689 ChEBI	decanoate	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
32217	17234 ChEBI	glucose	+	carbon source
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
32217	24996 ChEBI	lactate	+	carbon source
32217	25017 ChEBI	leucine	+	carbon source
32217	25115 ChEBI	malate	+	carbon source
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
32217	17306 ChEBI	maltose	+	carbon source
32217	29864 ChEBI	mannitol	+	carbon source
32217	37684 ChEBI	mannose	+	carbon source
32217	506227 ChEBI	N-acetylglucosamine	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
32217	18401 ChEBI	phenylacetate	+	carbon source
32217	17992 ChEBI	sucrose	+	carbon source
32217	27082 ChEBI	trehalose	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
32217	53426 ChEBI	tween 80	+	carbon source
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
32217	acid phosphatase	+	3.1.3.2
32217	alkaline phosphatase	+	3.1.3.1
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
17236	catalase	+	1.11.1.6
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
17236	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	quinate degradation	100	2 of 2
66794	ethanol fermentation	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	Entner Doudoroff pathway	100	10 of 10
66794	gallate degradation	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	glycogen metabolism	100	5 of 5
66794	pentose phosphate pathway	100	11 of 11
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	4-hydroxymandelate degradation	100	9 of 9
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	octane oxidation	100	3 of 3
66794	valine metabolism	100	9 of 9
66794	resorcinol degradation	100	2 of 2
66794	acetate fermentation	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	starch degradation	100	10 of 10
66794	ppGpp biosynthesis	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	ubiquinone biosynthesis	100	7 of 7
66794	taurine degradation	100	1 of 1
66794	aerobactin biosynthesis	100	1 of 1
66794	coenzyme A metabolism	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	cyanate degradation	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	ribulose monophosphate pathway	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	leucine metabolism	92.31	12 of 13
66794	vitamin B12 metabolism	91.18	31 of 34
66794	proline metabolism	90.91	10 of 11
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	pyrimidine metabolism	86.67	39 of 45
66794	alanine metabolism	86.21	25 of 29
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	citric acid cycle	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	phenol degradation	85	17 of 20
66794	vitamin B1 metabolism	84.62	11 of 13
66794	cysteine metabolism	83.33	15 of 18
66794	glycolysis	82.35	14 of 17
66794	degradation of pentoses	82.14	23 of 28
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	methionine metabolism	80.77	21 of 26
66794	myo-inositol biosynthesis	80	8 of 10
66794	vitamin K metabolism	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	3-phenylpropionate degradation	80	12 of 15
66794	hydrogen production	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	degradation of sugar acids	80	20 of 25
66794	purine metabolism	79.79	75 of 94
66794	arginine metabolism	79.17	19 of 24
66794	tyrosine metabolism	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	sulfate reduction	76.92	10 of 13
66794	phosphatidylethanolamine bioynthesis	76.92	10 of 13
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	carnitine metabolism	75	6 of 8
66794	ketogluconate metabolism	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	cyclohexanol degradation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	lysine metabolism	73.81	31 of 42
66794	flavin biosynthesis	73.33	11 of 15
66794	d-xylose degradation	72.73	8 of 11
66794	histidine metabolism	72.41	21 of 29
66794	propanol degradation	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	oxidative phosphorylation	70.33	64 of 91
66794	4-hydroxyphenylacetate degradation	70	7 of 10
66794	propionate fermentation	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	degradation of sugar alcohols	68.75	11 of 16
66794	androgen and estrogen metabolism	68.75	11 of 16
66794	lipid metabolism	67.74	21 of 31
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	polyamine pathway	65.22	15 of 23
66794	metabolism of disaccharids	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	phenylpropanoid biosynthesis	61.54	8 of 13
66794	degradation of hexoses	61.11	11 of 18
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	nitrate assimilation	55.56	5 of 9
66794	cholesterol biosynthesis	54.55	6 of 11
66794	ascorbate metabolism	54.55	12 of 22
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	bile acid biosynthesis, neutral pathway	52.94	9 of 17
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	coenzyme M biosynthesis	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	kanosamine biosynthesis II	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	glycine betaine biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	elloramycin biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	carotenoid biosynthesis	36.36	8 of 22
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	sphingosine metabolism	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	chlorophyll metabolism	27.78	5 of 18
66794	methanogenesis from CO2	25	3 of 12
66794	alginate biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
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
17236	-	-	-	-	-	+	-	+	+	+	+	+	+	+	+	+	+	+	-	+	+
17236	-	-	-	-	-	-	-	+	+	+	+	+	+	-	+/-	+/-	-	+	-	+	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Moss

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Sampling date
17236	Aulacomnium palustre	Aulacomnium palustre	Graal-Müritz, Ribnitzer Großes Moor	Germany	DEU	Europe
59778	Mosses/lichens (Aulacomnium palustre)			Germany	DEU	Europe	2002-03-01

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17236	1	Risk group (German 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	ASM755681v1 assembly for Paraburkholderia megapolitana LMG 23650	complete	GCA_007556815	420953.7	8114320692	420953	97.33
66792	IMG-taxon 2671180118 annotated assembly for Paraburkholderia megapolitana LMG 23650	contig	GCA_900113825	420953.5	2671180118	420953	71.96

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17236	Burkholderia megapolitana 16S rRNA, strain LMG 23650T	AM489502	1483		420953

GC content

32217

GC-content (mol%)61.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paraburkholderia megapolitana strain LMG 23650
PATRIC: 420953.7

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	85.80	no
125439	motility	BacteriaNetⓘ	yes	57.80	no
125439	gram_stain	BacteriaNetⓘ	negative	75.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paraburkholderia megapolitana LMG 23650
NCBI: GCA_007556815.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.50	no
125438	anaerobic	anaerobicⓘ	no	96.00	yes
125438	aerobic	aerobicⓘ	yes	90.39	yes
125438	spore-forming	spore-formingⓘ	no	87.59	yes
125438	thermophilic	thermophileⓘ	no	98.50	yes
125438	flagellated	motile2+ⓘ	yes	78.64	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Discovery of megapolipeptins by genome mining of a Burkholderiales bacteria collection.	Paulo BS, Recchia MJJ, Lee S, Fergusson CH, Romanowski SB, Hernandez A, Krull N, Liu DY, Cavanagh H, Bos A, Gray CA, Murphy BT, Linington RG, Eustaquio AS.	Chem Sci	10.1039/d4sc03594a	2024
	Mining for novel antibiotics in the age of antimicrobial resistance.	Udaondo Z, Matilla MA.	Microb Biotechnol	10.1111/1751-7915.13662	2020
	Improved dsDNA recombineering enables versatile multiplex genome engineering of kilobase-scale sequences in diverse bacteria.	Wang X, Zheng W, Zhou H, Tu Q, Tang YJ, Stewart AF, Zhang Y, Bian X.	Nucleic Acids Res	10.1093/nar/gkab1076	2022
	Biotechnology approaches for natural product discovery, engineering, and production based on Burkholderia bacteria.	Adaikpoh BI, Fernandez HN, Eustaquio AS.	Curr Opin Biotechnol	10.1016/j.copbio.2022.102782	2022
	Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species.	Sawana A, Adeolu M, Gupta RS.	Front Genet	10.3389/fgene.2014.00429	2014
	Identification of Collimonas gene loci involved in the biosynthesis of a diffusible secondary metabolite with broad-spectrum antifungal activity and plant-protective properties.	Akum FN, Kumar R, Lai G, Williams CH, Doan HK, Leveau JHJ.	Microb Biotechnol	10.1111/1751-7915.13716	2021
Genetics	Establishment of recombineering genome editing system in Paraburkholderia megapolitana empowers activation of silent biosynthetic gene clusters.	Zheng W, Wang X, Zhou H, Zhang Y, Li A, Bian X	Microb Biotechnol	10.1111/1751-7915.13535	2020
Phylogeny	Burkholderia bryophila sp. nov. and Burkholderia megapolitana sp. nov., moss-associated species with antifungal and plant-growth-promoting properties.	Vandamme P, Opelt K, Knochel N, Berg C, Schonmann S, De Brandt E, Eberl L, Falsen E, Berg G	Int J Syst Evol Microbiol	10.1099/ijs.0.65142-0	2007

References

#17236	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23488
#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 )
#28459	IJSEM 2228 2007 ( DOI 10.1099/ijs.0.65142-0 , PubMed 17911288 )
#32217	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 #28459
#59778	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 53006
#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 )
#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 )

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Paraburkholderia megapolitana (DSM 23488, CCUG 53006, LMG 23650)

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

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_007556815

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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