Name: Paraburkholderia oxyphila OX-01
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 1991

Type strain:

Species: Paraburkholderia oxyphila

Strain Designation: OX-01

Culture col. no.: DSM 22550, LMG 26376, NBRC 105797, CIP 110291

Strain history: CIP <- 2011, H. Murata, Forestry and Forest Products Research Inst., Ibaraki, Japan: strain OX-01

NCBI tax ID(s): 1218083 (strain), 614212 (species)

SI-ID 376074

DSM 22550, NBRC 105797, LMG 26376, CIP 110291

Section

Paraburkholderia oxyphila OX-01 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from acidic forest soil.

Gram-negative
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 oxyphila**
	Full Scientific Name (LPSN)	Paraburkholderia oxyphila (Otsuka et al. 2011) Sawana et al. 2015

Synonym

Burkholderia oxyphila

Information on morphological and physiological properties Morphology

[Ref.: #29628]	Gram stain	negative
[Ref.: #121488]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.985

[Ref.: #29628]	Cell length	1.75 µm

[Ref.: #29628]	Cell width	0.85 µm

[Ref.: #29628]	Cell shape	rod-shaped
[Ref.: #121488]	Cell shape	rod-shaped

[Ref.: #29628]	Motility	no
[Ref.: #121488]	Motility	no
[Ref.: #69480]	Motility	yes Confidence in %93.32

[Ref.: #29628]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16390]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #16390]

Culture medium growth

[Ref.: #16390]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16390]

Culture medium composition

expand / minimize

[Ref.: #41968]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #41968]

Culture medium growth

[Ref.: #41968]

Culture medium composition

expand / minimize

[Ref.: #121488]

Culture medium

CIP Medium 368

[Ref.: #121488]

Culture medium growth

[Ref.: #121488]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #121488]

Culture medium

CIP Medium 72

[Ref.: #121488]

Culture medium growth

[Ref.: #121488]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #16390]	growth	28 °C
[Ref.: #29628]	growth	15-40 °C
[Ref.: #29628]	optimum	30 °C
[Ref.: #41968]	growth	30 °C

[Ref.: #16390]	Temperature range	mesophilic
[Ref.: #29628]	Temperature range	mesophilic
[Ref.: #41968]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29628]			optimum	5.75
[Ref.: #29628]			growth	3.5-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29628]	Oxygen tolerance	aerobe
[Ref.: #121488]	Oxygen tolerance	obligate aerobe

[Ref.: #29628]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29628]	2-dehydro-D-gluconate ChEBI	+	carbon source
[Ref.: #29628]	adipate ChEBI	+	carbon source
[Ref.: #68369]	adipate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #29628]	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.: #29628]	decanoate ChEBI	+	carbon source
[Ref.: #68369]	decanoate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #29628]	fructose ChEBI	+	carbon source
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #29628]	gluconate ChEBI	+	carbon source
[Ref.: #68369]	gluconate ChEBI	+	assimilation	* from API 20NE
[Ref.: #29628]	glucose ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #29628]	L-arabitol ChEBI	+	carbon source
[Ref.: #29628]	malate ChEBI	+	carbon source
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #29628]	mannitol ChEBI	+	carbon source
[Ref.: #29628]	mannose ChEBI	+	carbon source
[Ref.: #29628]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #121488]	nitrate ChEBI	-	reduction
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #121488]	nitrite ChEBI	-	reduction
[Ref.: #29628]	phenylacetate ChEBI	+	carbon source
[Ref.: #29628]	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.: #121488]		indole ChEBI	no
[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.: #29628]	acid phosphatase	+	3.1.3.2
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #29628]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym, API 20NE
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #29628]	catalase	+	1.11.1.6
[Ref.: #121488]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68369]	cytochrome oxidase	-	1.9.3.1	* from API 20NE
[Ref.: #16390]	cytochrome-c oxidase	-	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #121488]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #29628]	urease	+	3.5.1.5
[Ref.: #121488]	urease	+	3.5.1.5
[Ref.: #68369]	urease	+	3.5.1.5	* from API 20NE
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #16390]	23848	-	-	-	-	+	-	-	-	+	-	+	+	+	-	+	+	+	+	+	+	-

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #121488]	12494	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #16390]	Sample type/isolated from	acidic forest soil
[Ref.: #16390]	Geographic location (country and/or sea, region)	Ibaraki, Tsukuba
[Ref.: #16390]	Country	Japan
[Ref.: #16390]	Country ISO 3 Code	JPN
[Ref.: #16390]	Continent	Asia

[Ref.: #121488]	Sample type/isolated from	Environment, Soil, acidic forest
[Ref.: #121488]	Geographic location (country and/or sea, region)	Ibaraki
[Ref.: #121488]	Country	Japan
[Ref.: #121488]	Country ISO 3 Code	JPN
[Ref.: #121488]	Continent	Asia
[Ref.: #121488]	Isolation date	2008
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil
#Condition	#Acidic	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB682297 (>99% sequence identity) for Paraburkholderia oxyphila from Microbeatlas

Aquatic Samples	41
Soil Samples	119
Animal Samples	17
Plant Samples	31
Total Samples	208

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

[Ref.: #16390]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121488]	Biosafety level	1	Risk group (French classification)

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

16S Sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #16390]	Burkholderia oxyphila gene for 16S ribosomal RNA, partial sequence, clone: pCR2.1::OX-01_rDNA#4	AB488693	1455	ENA	1218083 tax ID
[Ref.: #20218]	Burkholderia oxyphila gene for 16S rRNA, partial sequence, strain: NBRC 105797	AB682297	1458	ENA	1218083 tax ID	*
[Ref.: #20218]	Burkholderia oxyphila gene for 16S ribosomal RNA, partial sequence, clone: pCR2.1::OX-01_rDNA#2	AB488692	1455	ENA	1218083 tax ID	*
[Ref.: #20218]	Burkholderia oxyphila gene for 16S ribosomal RNA, partial sequence, clone: pCR2.1::OX-01_rDNA#5	AB488694	1455	ENA	1218083 tax ID	*
[Ref.: #20218]	Burkholderia oxyphila gene for 16S ribosomal RNA, partial sequence, clone: pCR2.1::OX-01_rDNA#7	AB488695	1455	ENA	1218083 tax ID	*
[Ref.: #20218]	Burkholderia oxyphila gene for 16S ribosomal RNA, partial sequence, clone: pCR2.1::OX-01_rDNA#8	AB488696	1455	ENA	1218083 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paraburkholderia oxyphila NBRC 105797	GCA_000685075	contig	GenBank	1218083 tax ID	*
[Ref.: #66792]	Burkholderia oxyphila NBRC 105797	1218083.4	wgs	PATRIC	1218083 tax ID	*
[Ref.: #66792]	Paraburkholderia oxyphila NBRC 105797	2579778781	draft	JGI IMG/M	1218083 tax ID	*

[Ref.: #16390]	GC-content	64 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29628]	GC-content	64 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: Burkholderia oxyphila NBRC 105797 PATRIC: 1218083.4
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Burkholderia oxyphila NBRC 105797 PATRIC: 1218083.4
[Ref.: #69480]	motile	yes	86.603	yes
[Ref.: #69480]	gram-positive	no	98.03	no
[Ref.: #69480]	anaerobic	no	97.856	no
[Ref.: #69480]	aerobic	yes	86.057	yes
[Ref.: #69480]	halophile	no	93.194	no
[Ref.: #69480]	spore-forming	no	92.517	yes
[Ref.: #69480]	glucose-util	yes	90.751	yes
[Ref.: #69480]	flagellated	no	77.394	no
[Ref.: #69480]	thermophile	no	99.698	yes
[Ref.: #69480]	glucose-ferment	no	87.944	yes

Availability in culture collections External links

[Ref.: #16390]

Culture collection no.

DSM 22550, LMG 26376, NBRC 105797, CIP 110291

[Ref.: #71638]

SI-ID 376074

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paraburkholderia pallida sp. nov. and Paraburkholderia silviterrae sp. nov., isolated from forest soil.	Xiao SY, Gao ZH, Lin QH, Qiu LH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003681	2019	*
Phylogeny	Paraburkholderia dokdonella sp. nov., isolated from a plant from the genus Campanula.	Jung MY, Kang MS, Lee KE, Lee EY, Park SJ	J Microbiol	10.1007/s12275-019-8500-5	2018	*
Metabolism	Enzymatic activity of cell-free extracts from Burkholderia oxyphila OX-01 bio-converts (+)-catechin and (-)-epicatechin to (+)-taxifolin.	Otsuka Y, Matsuda M, Sonoki T, Sato-Izawa K, Goodell B, Jelison J, Navarro RR, Murata H, Nakamura M	Biosci Biotechnol Biochem	10.1080/09168451.2016.1220822	2016	*
Phylogeny	Paraburkholderia caffeinitolerans sp. nov., a caffeine degrading species isolated from a tea plantation soil sample.	Gao ZQ, Zhao DY, Xu L, Zhao RT, Chen M, Zhang CZ	Antonie Van Leeuwenhoek	10.1007/s10482-016-0749-7	2016	*
Phylogeny	Burkholderia oxyphila sp. nov., a bacterium isolated from acidic forest soil that catabolizes (+)-catechin and its putative aromatic derivatives.	Otsuka Y, Muramatsu Y, Nakagawa Y, Matsuda M, Nakamura M, Murata H	Int J Syst Evol Microbiol	10.1099/ijs.0.017368-0	2010	*

References

#16390

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22550

#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 )

#29628

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 #26018 (see below)

#41968 ; Curators of the CIP;

#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 .

#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 )

#71638

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-ID376074.1 )

#121488 Collection of Institut Pasteur ; Curators of the CIP; CIP 110291

#26018

IJSEM 249 2011 ( DOI 10.1099/ijs.0.017368-0 , PubMed 20207808 )

* These data were automatically processed and therefore are not curated

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Burkholderia oxyphila NBRC 105797

Burkholderia oxyphila NBRC 105797

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