Name: Paraburkholderia sediminicola HU2-65W
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 1982

Type strain:

Species: Paraburkholderia sediminicola

Strain Designation: HU2-65W

Culture col. no.: DSM 21400, KCTC 22086, LMG 24238, CCUG 56490

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 458836 (species)

SI-ID 343366

LMG 24238, KCTC 22086, DSM 21400

Section

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

Gram-negative
motile
rod-shaped
aerobe
mesophilic
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	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Burkholderiaceae*
	Genus	*Paraburkholderia*
	Species	**Paraburkholderia sediminicola**
	Full Scientific Name (LPSN)	Paraburkholderia sediminicola (Lim et al. 2008) Sawana et al. 2015

Synonym

Burkholderia sediminicola

Information on morphological and physiological properties Morphology

[Ref.: #32441]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.986

[Ref.: #32441]	Cell length	1 µm

[Ref.: #32441]	Cell width	0.4 µm

[Ref.: #32441]	Cell shape	rod-shaped

[Ref.: #32441]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %92.623

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15678]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #15678]

Culture medium growth

[Ref.: #15678]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15678]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #15678]	growth	28 °C
[Ref.: #32441]	growth	15-30 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #15678]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32441]			growth	06-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %99
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.997

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32441]		NaCl		growth	0-1.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32441]	2-dehydro-D-gluconate ChEBI	+	carbon source
[Ref.: #32441]	3-hydroxybenzoate ChEBI	+	carbon source
[Ref.: #32441]	4-hydroxybenzoate ChEBI	+	carbon source
[Ref.: #32441]	alanine ChEBI	+	carbon source
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #32441]	citrate ChEBI	+	carbon source
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #32441]	fucose ChEBI	+	carbon source
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #32441]	histidine ChEBI	+	carbon source
[Ref.: #32441]	malate ChEBI	+	carbon source
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #32441]	phenylacetate ChEBI	+	carbon source
[Ref.: #32441]	proline ChEBI	+	carbon source
[Ref.: #32441]	ribose ChEBI	+	carbon source
[Ref.: #32441]	sorbitol ChEBI	+	carbon source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #15678]	catalase	+	1.11.1.6
[Ref.: #32441]	catalase	+	1.11.1.6
[Ref.: #32441]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #15678]	cytochrome-c oxidase	+	1.9.3.1
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

API® 20NE:

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

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #15678]	23826	-	-	-	-	-	-	-	+	+	+/-	+	+	+	-	-	+	+/-	+	+	+	+

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

[Ref.: #15678]	Sample type/isolated from	freshwater sediment
[Ref.: #15678]	Country	Republic of Korea
[Ref.: #15678]	Country ISO 3 Code	KOR
[Ref.: #15678]	Continent	Asia

[Ref.: #60989]	Sample type/isolated from	Freshwater sediment
[Ref.: #60989]	Geographic location (country and/or sea, region)	Daejeon
[Ref.: #60989]	Country	Republic of Korea
[Ref.: #60989]	Country ISO 3 Code	KOR
[Ref.: #60989]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From freshwater sediment
[Ref.: #67771]	Geographic location (country and/or sea, region)	Daejeon
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Sediment
#Environmental	#Aquatic	#Freshwater

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #15678]

Biosafety level

Risk group (German classification)
According to TRBA 466

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

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #15678]	Burkholderia sediminicola strain HU2-65W 16S ribosomal RNA gene, partial sequence	EU035613	1473	ENA	458836 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paraburkholderia sediminicola LMG 24238	GCA_902859805	contig	GenBank	458836 tax ID	*
[Ref.: #66792]	Paraburkholderia sediminicola strain LMG 24238	458836.10	wgs	PATRIC	458836 tax ID	*
[Ref.: #66792]	Paraburkholderia sediminicola strain LMG 24238	458836.8	wgs	PATRIC	458836 tax ID	*

[Ref.: #15678]	GC-content	61.2 mol%	high performance liquid chromatography (HPLC)
[Ref.: #32441]	GC-content	61.2 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Paraburkholderia sediminicola strain LMG 24238 PATRIC: 458836.8
[Ref.: #69481]	spore-forming	no	99	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paraburkholderia sediminicola strain LMG 24238 PATRIC: 458836.10
[Ref.: #69480]	gram-positive	no	98.231	yes
[Ref.: #69480]	anaerobic	no	98.6	no
[Ref.: #69480]	halophile	no	93.824	yes
[Ref.: #69480]	spore-forming	no	94.237	no
[Ref.: #69480]	glucose-util	yes	93.315	yes
[Ref.: #69480]	aerobic	yes	87.154	yes
[Ref.: #69480]	flagellated	no	84.648	no
[Ref.: #69480]	thermophile	no	99.634	no
[Ref.: #69480]	motile	yes	86.119	no
[Ref.: #69480]	glucose-ferment	no	88.107	yes

Availability in culture collections External links

[Ref.: #15678]

Culture collection no.

DSM 21400, KCTC 22086, LMG 24238, CCUG 56490

[Ref.: #71628]	SI-ID 343366	*
[Ref.: #71629]	SI-ID 408726	*

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 )

#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 (see below)

#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 .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#71628

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-ID343366.1 )

#71629

#28663

IJSEM 565 2008 ( DOI 10.1099/ijs.0.65502-0 , PubMed 18319455 )

* These data were automatically processed and therefore are not curated

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Paraburkholderia sediminicola strain LMG 24238

Paraburkholderia sediminicola strain LMG 24238

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