Paraburkholderia phenoliruptrix (DSM 17773, CCUG 48558, CIP 108591)

Name: Paraburkholderia phenoliruptrix (DSM 17773, CCUG 48558, CIP 108591)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1967

Type strain

Strain Designation AC1100

Culture col. no. DSM 17773 CCUG 48558 CIP 108591 LMG 22037 AC1100

NCBI tax ID(s) 252970

Special Collections DSMZ CCUG CIP

History DSMZ <- CCUG <- LMG <- T. Coenye, Gent <- D. Henry, Univ. British Columbia, Vancouver, Canada CIP <- 2004, CCUG <- 2003, LMG <- 2003, T. Coenye, Ghent Univ., Ghent, Belgium <- 1999, D. Henry, British Columbia Univ., Vancouver, Canada: strain AC1100

Links

Paraburkholderia phenoliruptrix AC1100 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from chemostat with 2,4,5-trichlorophenoxyacetic acid.

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

Name and taxonomic classification

SI-ID 43466

ATCC 53867,ATCC 39027,LMG22037,CCUG 48558,CIP 108591,DSM 17773

@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 phenoliruptrix

Full scientific name Paraburkholderia phenoliruptrix (Coenye et al. 2005) Sawana et al. 2015

Synonyms (1)

Burkholderia phenoliruptrix

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
121796	negative	rod-shaped
125438	negative			97.469

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7177	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
7177	MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457)	Medium recipe at MediaDive	Name: MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457) Composition: Na2HPO4 2.44 g/l KH2PO4 1.52 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.05 g/l EDTA 0.005 g/l FeSO4 x 7 H2O 0.002 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water
41977	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121796	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7177	positive	growth	28
41977	positive	growth	30
58230	positive	growth	30
121796	positive	growth	25-37
121796	negative	growth	5
121796	negative	growth	10
121796	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
58230	aerobe
121796	obligate aerobe
125439	obligate aerobe	99.646

Spore formation

@ref	Spore formation	Confidence
125439		97.754

Halophily

@ref	Salt	Growth	Tested relation	Concentration
121796	NaCl	positive	growth	0-2 %
121796	NaCl		growth	4 %
121796	NaCl		growth	6 %
121796	NaCl		growth	8 %
121796	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
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
121796	4853 ChEBI	esculin	-	hydrolysis
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
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
121796	17632 ChEBI	nitrate	-	reduction
121796	17632 ChEBI	nitrate	-	respiration
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
121796	16301 ChEBI	nitrite	-	reduction
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
121796	35581 ChEBI	indole

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
121796	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
121796	amylase	+
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
121796	beta-galactosidase	+	3.2.1.23
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
121796	caseinase	-	3.4.21.50
121796	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
121796	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
121796	gelatinase	-
68369	gelatinase	-		from API 20NE
121796	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
121796	lipase	-
68382	lipase (C 14)	-		from API zym
121796	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
121796	ornithine decarboxylase	-	4.1.1.17
121796	oxidase	+
121796	protease	-
68382	trypsin	-	3.4.21.4	from API zym
121796	tryptophan deaminase	-
121796	tween esterase	-
121796	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
121796	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	+	-	-	-	-

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
7177	-	-	-	-	-	-	-	+	+	+	+	+	+	-	+	+/-	+/-	+	+	+	+/-

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
121796	not determinedn.d.	+	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	+	-	+	+	-	-	-	-	+	-	-	-	+	-	-	+	+	+	-	+	-	+	+	-	-	-	-	-	-	-	-	+	+	-	+	-	-	-	-	-	+	-	-	-	-	-	+	-	+	+	-	-	-	-	+	-	-	+	+	-	-	-	-	-	-	-	+	+	-	+	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Engineered	#Bioreactor

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7177	chemostat with 2,4,5-trichlorophenoxyacetic acid	Illionis	USA	USA	North America
58230	Chemostat grown with 2,4,5-trichlorophenoxyacetic	Vancouver	Canada	CAN	North America
121796	Chemostat grown with 2 4 5-trichlorophenoxyacetic	Vancouver	Canada	CAN	North America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7177	1	Risk group (German classification) According to TRBA 466
121796	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	LMG 22037 assembly for Paraburkholderia phenoliruptrix LMG 22037	contig	GCA_902859825	252970.3	8115456804	252970	53.5
66792	ASM90283365v1 assembly for Paraburkholderia phenoliruptrix LMG 22037	contig	GCA_902833655	252970.5	8111924950	252970	12.19
66792	Velvet for BPAC1100 assembly for Paraburkholderia phenoliruptrix AC1100	contig	GCA_000416445	1337996.4	2554235175	1337996	0

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Burkholderia phenoliruptrix strain LMG 22037 16S ribosomal RNA gene, partial sequence	HQ849094	1126		252970
7177	Burkholderia sp. AC1100 16S ribosomal RNA gene, partial sequence	AY435213	1485		252970

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: LMG 22037 assembly for Paraburkholderia phenoliruptrix LMG 22037
BV-BRC: 252970.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.65	no
125439	gram_stain	BacteriaNetⓘ	negative	89.98	no
125439	motility	BacteriaNetⓘ	yes	54.40	no
125439	spore_formation	BacteriaNetⓘ	no	97.75	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paraburkholderia phenoliruptrix strain LMG 22037
PATRIC: 252970.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.47	no
125438	anaerobic	anaerobicⓘ	no	96.51	yes
125438	spore-forming	spore-formingⓘ	no	86.62	no
125438	aerobic	aerobicⓘ	yes	86.00	yes
125438	thermophilic	thermophileⓘ	no	98.44	yes
125438	flagellated	motile2+ⓘ	yes	84.79	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
	Genomic Assemblies of Members of Burkholderia and Related Genera as a Resource for Natural Product Discovery.	Mullins AJ, Jones C, Bull MJ, Webster G, Parkhill J, Connor TR, Murray JAH, Challis GL, Mahenthiralingam E.	Microbiol Resour Announc	10.1128/mra.00485-20	2020
Metabolism	Catalytic mechanism of 5-chlorohydroxyhydroquinone dehydrochlorinase from the YCII superfamily of largely unknown function.	Hayes RP, Lewis KM, Xun L, Kang C	J Biol Chem	10.1074/jbc.M113.499368	2013
Genetics	Genome Sequence of the 2,4,5-Trichlorophenoxyacetate-Degrading Bacterium Burkholderia phenoliruptrix Strain AC1100.	Xu P, Yu H, Chakrabarty AM, Xun L	Genome Announc	10.1128/genomeA.00600-13	2013
Phylogeny	Burkholderia phenoliruptrix sp. nov., to accommodate the 2,4,5-trichlorophenoxyacetic acid and halophenol-degrading strain AC1100.	Coenye T, Henry D, Speert DP, Vandamme P	Syst Appl Microbiol	10.1078/0723202042369992	2004

References

#7177	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17773
#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 )
#41977	; Curators of the CIP;
#58230	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 48558
#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 .
#121796	Collection of Institut Pasteur ; Curators of the CIP; CIP 108591
#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

About us

Paraburkholderia phenoliruptrix (DSM 17773, CCUG 48558, CIP 108591)

Name and taxonomic classification

Morphology

Cell 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_902859825

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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