Paraburkholderia sediminicola (DSM 21400, KCTC 22086, LMG 24238)

Name: Paraburkholderia sediminicola (DSM 21400, KCTC 22086, LMG 24238)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1982

Type strain

Strain Designation HU2-65W

Culture col. no. DSM 21400 KCTC 22086 LMG 24238 CCUG 56490 HU2-65W

NCBI tax ID(s) 458836

Special Collections DSMZ CCUG KCTC Literature strains

History DSMZ <- KCTC/KRIBB; HU2-65W {2008} <- S. T. Lee KCTC <- ST Lee, KAIST

Links

Paraburkholderia sediminicola HU2-65W is an aerobe, Gram-negative, motile bacterium that was isolated from freshwater sediment.

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

Name and taxonomic classification

SI-ID 343366

LMG 24238,KCTC 22086,DSM 21400

@ref 20215

Last LPSN update 2026-05-29 08:25:23

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Burkholderiaceae

Genus Paraburkholderia

Species Paraburkholderia sediminicola

Full scientific name Paraburkholderia sediminicola (Lim et al. 2008) Sawana et al. 2015

Synonyms (1)

Burkholderia sediminicola

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
32441	negative	1 µm	0.4 µm	rod-shaped
67771	negative
125438	negative				96.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15678	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)
15678	positive	growth	28
32441	positive	growth	15-30
67771	positive	growth	30

Culture pH

@ref	Ability	Type	PH
32441	positive	growth	06-08

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
67771	aerobe
125439	obligate aerobe	98.603

Spore formation

@ref	Spore formation	Confidence
125439		95.934

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32441	NaCl	positive	growth	0-1.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32441	16808 ChEBI	2-dehydro-D-gluconate	+	carbon source
32441	16193 ChEBI	3-hydroxybenzoate	+	carbon source
32441	17879 ChEBI	4-hydroxybenzoate	+	carbon source
32441	16449 ChEBI	alanine	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
32441	16947 ChEBI	citrate	+	carbon source
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
32441	33984 ChEBI	fucose	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
32441	27570 ChEBI	histidine	+	carbon source
32441	25115 ChEBI	malate	+	carbon source
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
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
32441	18401 ChEBI	phenylacetate	+	carbon source
32441	26271 ChEBI	proline	+	carbon source
32441	33942 ChEBI	ribose	+	carbon source
32441	30911 ChEBI	sorbitol	+	carbon source
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
15678	catalase	+	1.11.1.6
32441	catalase	+	1.11.1.6
32441	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
15678	cytochrome-c oxidase	+	1.9.3.1
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

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
15678	-	-	-	-	-	-	-	+	+	+/-	+	+	+	-	-	+	+/-	+	+	+	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Sediment
#Environmental	#Aquatic	#Freshwater

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15678	freshwater sediment		Republic of Korea	KOR	Asia
60989	Freshwater sediment	Daejeon	Republic of Korea	KOR	Asia
67771	From freshwater sediment	Daejeon	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence EU035613 (>99% sequence identity) for Paraburkholderia from Microbeatlas

Aquatic Samples	246
Soil Samples	1715
Animal Samples	635
Plant Samples	226
Total Samples	2822

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15678	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	LMG 24238 assembly for Paraburkholderia sediminicola LMG 24238	contig	GCA_902859805	458836.10	2996269430	458836	71.63
66792	IMG-taxon 2654588104 annotated assembly for Paraburkholderia sediminicola	scaffold	GCA_900104005	458836.8		458836	0

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15678	Burkholderia sediminicola strain HU2-65W 16S ribosomal RNA gene, partial sequence	EU035613	1473		458836

GC content

@ref	GC-content (mol%)	Method
15678	61.2	high performance liquid chromatography (HPLC)
32441	61.2

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: LMG 24238 assembly for Paraburkholderia sediminicola LMG 24238
NCBI: GCA_902859805

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.60	no
125439	gram_stain	BacteriaNetⓘ	negative	65.44	no
125439	motility	BacteriaNetⓘ	yes	52.86	no
125439	spore_formation	BacteriaNetⓘ	no	95.93	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paraburkholderia sediminicola strain LMG 24238
PATRIC: 458836.10

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.50	no
125438	anaerobic	anaerobicⓘ	no	96.16	yes
125438	spore-forming	spore-formingⓘ	no	85.57	no
125438	aerobic	aerobicⓘ	yes	89.74	yes
125438	thermophilic	thermophileⓘ	no	97.49	yes
125438	flagellated	motile2+ⓘ	yes	83.94	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	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
	The Potato Yam Phyllosphere Ectosymbiont Paraburkholderia sp. Msb3 Is a Potent Growth Promotor in Tomato.	Herpell JB, Schindler F, Bejtovic M, Fragner L, Diallo B, Bellaire A, Kublik S, Foesel BU, Gschwendtner S, Kerou M, Schloter M, Weckwerth W.	Front Microbiol	10.3389/fmicb.2020.00581	2020
Phylogeny	Paraburkholderia caffeinilytica sp. nov., isolated from the soil of a tea plantation.	Gao Z, Yuan Y, Xu L, Liu R, Chen M, Zhang C	Int J Syst Evol Microbiol	10.1099/ijsem.0.001333	2016
Phylogeny	Burkholderia sediminicola sp. nov., isolated from freshwater sediment.	Lim JH, Baek SH, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.65502-0	2008

References

#15678	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21400
#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 )
#28663	IJSEM 565 2008 ( DOI 10.1099/ijs.0.65502-0 , PubMed 18319455 )
#32441	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 #28663
#60989	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 56490
#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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68369	Automatically annotated from API 20NE .
#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 .
#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 )

Content

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Paraburkholderia sediminicola (DSM 21400, KCTC 22086, LMG 24238)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_902859805

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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