Cupriavidus pinatubonensis (DSM 19553, CIP 108725, PNCM 10346)

Name: Cupriavidus pinatubonensis (DSM 19553, CIP 108725, PNCM 10346)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2053

Type strain

Strain Designation 1245

Culture col. no. DSM 19553 CIP 108725 PNCM 10346 CCUG 53907 1245 1 more

NCBI tax ID(s) 248026

Special Collections DSMZ CCUG CIP Literature strains KCTC

History DSMZ <- H. Ohta, Ibaraki University, Japan CIP <- 2005, H. Ohta, Ibaraki Univ., Ibaraki, Japan: strain 1245 CIP <- 2005, H. Ohta, Ibaraki Univ., Ibaraki, Japan: strain 1245

Links

Cupriavidus pinatubonensis 1245 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from volcanic ash deposits.

Gram-negative rod-shaped colony-forming aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 290966

CIP 108725,CCUG 53907,DSM 19553,LMG23994,LMG 23956,KCTC 22125

@ref 20215

Last LPSN update 2026-05-29 08:25:24

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Burkholderiaceae

Genus Cupriavidus

Species Cupriavidus pinatubonensis

Full scientific name Cupriavidus pinatubonensis Sato et al. 2006

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
23160	negative	0.8-1.6 µm	0.3-0.6 µm	rod-shaped
121833	negative			rod-shaped
125439	negative				97.27

Colony morphology

@ref	Colony color	Colony shape	Medium used	Hemolysis ability
23160	white	circular	100-fold diluted NB agar
121833				0

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
23160	100-fold diluted NB agar
38304	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121833	CIP Medium 72	Medium recipe at CIP
8170	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
8170	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
8170	TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)	Medium recipe at MediaDive	Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
8170	positive	growth	28
23160	positive	growth	27-41
38304	positive	growth	30
60075	positive	growth	37
121833	positive	growth	25-37
121833	negative	growth	5
121833	negative	growth	15
121833	negative	growth	41
121833	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
23160	aerobe
60075	aerobe
121833	obligate aerobe
125439	obligate aerobe	97.966

Spore formation

@ref	Spore formation	Confidence
23160
125439		99.523

Halophily

@ref	Salt	Growth	Tested relation	Concentration
121833	NaCl	positive	growth	0-10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23160	17879 ChEBI	4-hydroxybenzoate	+	assimilation
23160	30089 ChEBI	acetate	+	assimilation
23160	17128 ChEBI	adipate	+	assimilation
68369	17128 ChEBI	adipate	+	assimilation	from API 20NE
23160	22599 ChEBI	arabinose	-	assimilation
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
23160	18135 ChEBI	catechol	+	assimilation
23160	16947 ChEBI	citrate	+	assimilation
121833	16947 ChEBI	citrate	+	carbon source
23160	15824 ChEBI	D-fructose	+	assimilation
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
23160	27689 ChEBI	decanoate	+	assimilation
68369	27689 ChEBI	decanoate	+	assimilation	from API 20NE
121833	4853 ChEBI	esculin	-	hydrolysis
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
23160	29749 ChEBI	ferulate	-	assimilation
23160	15740 ChEBI	formate	-	assimilation
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
23160	24265 ChEBI	gluconate	+	assimilation
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
23160	17234 ChEBI	glucose	-	assimilation
23160	17234 ChEBI	glucose	-	builds acid from
23160	29987 ChEBI	glutamate	+	assimilation
23160	28591 ChEBI	guaiacol	-	assimilation
121833	606565 ChEBI	hippurate	+	hydrolysis
23160	24996 ChEBI	lactate	+	assimilation
23160	25115 ChEBI	malate	+	assimilation
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
121833	15792 ChEBI	malonate	+	assimilation
23160	17306 ChEBI	maltose	-	assimilation
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
23160	29864 ChEBI	mannitol	-	assimilation
23160	37684 ChEBI	mannose	-	assimilation
23160	506227 ChEBI	N-acetylglucosamine	-	assimilation
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
23160	17632 ChEBI	nitrate	+	reduction
121833	17632 ChEBI	nitrate	-	builds gas from
121833	17632 ChEBI	nitrate	+	reduction
121833	17632 ChEBI	nitrate	-	respiration
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
121833	16301 ChEBI	nitrite	+	builds gas from
121833	16301 ChEBI	nitrite	-	reduction
23160	15882 ChEBI	phenol	+	assimilation
23160	18401 ChEBI	phenylacetate	+	assimilation
23160	36241 ChEBI	protocatechuate	+	assimilation
23160	30762 ChEBI	salicylate	+	assimilation
23160	17992 ChEBI	sucrose	-	assimilation
23160		trimethoxybenzoate	+	assimilation
23160	27897 ChEBI	tryptophan	-	energy source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
23160	16632 ChEBI	vanillate	-	assimilation

Metabolite production

@ref	Chebi-ID	Metabolite
23160	35581 ChEBI	indole
68369	35581 ChEBI	indole	from API 20NE
121833	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test	Voges-proskauer-test	Methylred-test
121833	15688 ChEBI	acetoin		-
121833	17234 ChEBI	glucose			-
23160	35581 ChEBI	indole	-
68369	35581 ChEBI	indole	-			from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
121833	alcohol dehydrogenase	-	1.1.1.1
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
121833	amylase	-
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
23160	beta-galactosidase	-	3.2.1.23
68382	beta-galactosidase	-	3.2.1.23	from API zym
121833	beta-galactosidase	-	3.2.1.23
23160	beta-glucosidase	-	3.2.1.21
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
121833	caseinase	-	3.4.21.50
23160	catalase	+	1.11.1.6
121833	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
23160	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
121833	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
121833	gamma-glutamyltransferase	+	2.3.2.2
121833	gelatinase	-
68369	gelatinase	-		from API 20NE
121833	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
121833	lipase	-
68382	lipase (C 14)	-		from API zym
121833	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
121833	ornithine decarboxylase	-	4.1.1.17
121833	oxidase	+
121833	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
23160	tryptophan deaminase	-	4.1.99.1
121833	tryptophan deaminase	-
121833	tween esterase	-
23160	urease	+	3.5.1.5
121833	urease	+	3.5.1.5
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
121833	-	+	+	+	-	+	+	-	-	-	+	+	-	-	-	-	-	-	-	-

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
8170	+	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	+	+	+	+	+
8170	+	-	-	-	+	-	-	-	-	+	-	-	-	-	+	+	+	+	+	+	+

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
121833	not determinedn.d.	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	+	-	-	-	+	+	+	+	+	-	-	-	-	+	-	+	+	+	+	+	+	+	+	-	+	-	-	-	-	-	+	+	+	+	+	+	+	+	-	-	-	-	+	+	+	+	+	-	+	+	+	+	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Dust
#Environmental	#Terrestrial	#Mud (Sludge)
#Environmental	#Terrestrial	#Volcanic

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
8170	volcanic ash deposits		Mt. Pinatubo	Philippines	PHL	Asia
23160	volcanic mudflow deposits derived from the eruption of Mt. Pinatubo	1991
60075	Volcanic mudflow	1998	Mt Pinatubo	Philippines	PHL	Asia
121833	Environment, Volcanic mudflow		Mount Pinatubo	Philippines	PHL	Asia	1998

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8170	1	Risk group (German classification) According to TRBA 466
121833	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM4265462v1 assembly for Cupriavidus pinatubonensis CCUG 53907	scaffold	GCA_042654625	248026	53.25

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8170	Cupriavidus pinatubonensis gene for 16S ribosomal RNA, strain: 1245	AB121221	1524		248026
124043	Cupriavidus pinatubonensis partial 16S rRNA gene, type strain CCUG53907T	FN597611	1392		248026

GC content

23160

GC-content (mol%)65.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM4265462v1 assembly for Cupriavidus pinatubonensis CCUG 53907
NCBI: GCA_042654625

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.97	no
125439	gram_stain	BacteriaNetⓘ	negative	97.27	no
125439	motility	BacteriaNetⓘ	yes	70.72	no
125439	spore_formation	BacteriaNetⓘ	no	99.52	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Pathogenicity	Mycotoxin Biodegradation Ability of the Cupriavidus Genus.	Al-Nussairawi M, Risa A, Garai E, Varga E, Szabo I, Csenki-Bakos Z, Kriszt B, Cserhati M.	Curr Microbiol	10.1007/s00284-020-02063-7	2020
Phylogeny	Cupriavidus pinatubonensis sp. nov. and Cupriavidus laharis sp. nov., novel hydrogen-oxidizing, facultatively chemolithotrophic bacteria isolated from volcanic mudflow deposits from Mt. Pinatubo in the Philippines.	Sato Y, Nishihara H, Yoshida M, Watanabe M, Rondal JD, Concepcion RN, Ohta H	Int J Syst Evol Microbiol	10.1099/ijs.0.63922-0	2006

References

#8170	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19553
#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 )
#23160	Yoshinori Sato, Hirofumi Nishihara, Masao Yoshida, Makiko Watanabe, Jose D. Rondal, Rogelio N. Concepcion, Hiroyuki Ohta: Cupriavidus pinatubonensis sp. nov. and Cupriavidus laharis sp. nov., novel hydrogen-oxidizing, facultatively chemolithotrophic bacteria isolated from volcanic mudflow deposits from Mt. Pinatubo in the Philippines. IJSEM 56: 973 - 978 2006 ( DOI 10.1099/ijs.0.63922-0 , PubMed 16627640 )
#38304	; Curators of the CIP;
#60075	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 53907
#68369	Automatically annotated from API 20NE .
#68382	Automatically annotated from API zym .
#121833	Collection of Institut Pasteur ; Curators of the CIP; CIP 108725
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Cupriavidus pinatubonensis (DSM 19553, CIP 108725, PNCM 10346)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_042654625

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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