Paraburkholderia oxyphila (DSM 22550, LMG 26376, NBRC 105797)

Name: Paraburkholderia oxyphila (DSM 22550, LMG 26376, NBRC 105797)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1991

Type strain

Strain Designation OX-01

Culture col. no. DSM 22550 LMG 26376 NBRC 105797 OX-01 CIP 110291

NCBI tax ID(s) 1218083 614212

Special Collections DSMZ Literature strains CIP

History <- Y. Otsuka, Forestry and Forest Products Res. Inst. (FFPRI), Tsukuba, Japan; OX-01 CIP <- 2011, H. Murata, Forestry and Forest Products Research Inst., Ibaraki, Japan: strain OX-01

Links

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

Gram-negative rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 376074

DSM 22550,NBRC 105797,LMG 26376,CIP 110291

@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 oxyphila

Full scientific name Paraburkholderia oxyphila (Otsuka et al. 2011) Sawana et al. 2015

Synonyms (1)

Burkholderia oxyphila

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29628	negative	1.75 µm	0.85 µm	rod-shaped
121488	negative			rod-shaped
125438	negative				98
125439	negative				94

Pigmentation

29628

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
16390	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
41968	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121488	CIP Medium 368	Medium recipe at CIP
121488	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
16390	positive	growth	28	mesophilic
29628	positive	growth	15-40
29628	positive	optimum	30	mesophilic
41968	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
29628	positive	optimum	5.75
29628	positive	growth	3.5-8	acidophile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29628	aerobe
121488	obligate aerobe
125439	aerobe	91.7

Spore formation

@ref	Spore formation	Confidence
29628
125439		96.4

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29628	16808 ChEBI	2-dehydro-D-gluconate	+	carbon source
29628	17128 ChEBI	adipate	+	carbon source
68369	17128 ChEBI	adipate	+	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
29628	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
29628	27689 ChEBI	decanoate	+	carbon source
68369	27689 ChEBI	decanoate	+	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
29628	28757 ChEBI	fructose	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
29628	24265 ChEBI	gluconate	+	carbon source
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
29628	17234 ChEBI	glucose	+	carbon source
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
29628	18403 ChEBI	L-arabitol	+	carbon source
29628	25115 ChEBI	malate	+	carbon source
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
29628	29864 ChEBI	mannitol	+	carbon source
29628	37684 ChEBI	mannose	+	carbon source
29628	506227 ChEBI	N-acetylglucosamine	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
121488	17632 ChEBI	nitrate	-	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
121488	16301 ChEBI	nitrite	-	reduction
29628	18401 ChEBI	phenylacetate	+	carbon source
29628	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
121488	35581 ChEBI	indole

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
29628	acid phosphatase	+	3.1.3.2
68382	acid phosphatase	+	3.1.3.2	from API zym
29628	alkaline phosphatase	+	3.1.3.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
29628	catalase	+	1.11.1.6
121488	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68369	cytochrome oxidase	-	1.9.3.1	from API 20NE
16390	cytochrome-c oxidase	-	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68369	gelatinase	-		from API 20NE
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
121488	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
29628	urease	+	3.5.1.5
121488	urease	+	3.5.1.5
68369	urease	+	3.5.1.5	from API 20NE
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
121488	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

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
16390	-	-	-	-	+	-	-	-	+	-	+	+	+	-	+	+	+	+	+	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil
#Condition	#Acidic	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
16390	acidic forest soil	Ibaraki, Tsukuba	Japan	JPN	Asia
121488	Environment, Soil, acidic forest	Ibaraki	Japan	JPN	Asia	2008

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16390	1	Risk group (German classification) According to TRBA 466
121488	1	Risk group (French 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	ASM68507v1 assembly for Paraburkholderia oxyphila NBRC 105797	contig	GCA_000685075	1218083.4	2579778781	1218083	15.37

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Burkholderia oxyphila gene for 16S rRNA, partial sequence, strain: NBRC 105797	AB682297	1458		1218083
16390	Burkholderia oxyphila gene for 16S ribosomal RNA, partial sequence, clone: pCR2.1::OX-01_rDNA#4	AB488693	1455		1218083

GC content

@ref	GC-content (mol%)	Method
16390	64	high performance liquid chromatography (HPLC)
29628	64

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paraburkholderia oxyphila NBRC 105797
NCBI: GCA_000685075

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.40	no
125439	motility	BacteriaNetⓘ	yes	67.10	no
125439	gram_stain	BacteriaNetⓘ	negative	94.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	91.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Burkholderia oxyphila NBRC 105797
PATRIC: 1218083.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.00	yes
125438	anaerobic	anaerobicⓘ	no	94.94	no
125438	spore-forming	spore-formingⓘ	no	86.92	no
125438	aerobic	aerobicⓘ	yes	89.86	yes
125438	thermophilic	thermophileⓘ	no	97.92	no
125438	flagellated	motile2+ⓘ	yes	84.37	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
	Genome-based taxonomy of Burkholderia sensu lato: Distinguishing closely related species.	Bach E, Volpiano CG, Sant'Anna FH, Passaglia LMP.	Genet Mol Biol	10.1590/1678-4685-gmb-2023-0122	2023
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 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
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 )
#26018	IJSEM 249 2011 ( DOI 10.1099/ijs.0.017368-0 , PubMed 20207808 )
#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
#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 .
#121488	Collection of Institut Pasteur ; Curators of the CIP; CIP 110291
#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 oxyphila (DSM 22550, LMG 26376, NBRC 105797)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000685075

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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