Pandoraea vervacti (DSM 23571, CCM 7667, NBRC 106088)

Name: Pandoraea vervacti (DSM 23571, CCM 7667, NBRC 106088)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2066

Type strain

Strain Designation 561, NS15

Culture col. no. DSM 23571 CCM 7667 NBRC 106088 561 NS15

NCBI tax ID(s) 656178

Special Collections DSMZ Literature strains

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Pandoraea vervacti 561 is a mesophilic, Gram-negative, motile prokaryote that was isolated from uncultivated field soil.

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

Name and taxonomic classification

SI-ID 378120

CCM 7667,DSM 23571,NBRC 106088,LMG 28170

@ref 20215

Last LPSN update 2025-12-16 09:47:15

Domain Pseudomonadati

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Burkholderiaceae

Genus Pandoraea

Species Pandoraea vervacti

Full scientific name Pandoraea vervacti Sahin et al. 2011

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
23368	negative	2.8 µm	0.9 µm	rod-shaped
125439	negative				90.5
125438	negative				98.5

Colony morphology

@ref	Colony size	Colony color	Incubation period	Medium used
17291			1-2 days
23368	1-2 mm	cream	2 days	TSA

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17291	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
23368	Trypticase Soy Agar (TSA)

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
17291	positive	growth	28	mesophilic
23368	positive	growth	30-42

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.6

Halophily

@ref	Salt	Growth	Tested relation	Concentration
23368	NaCl	positive	growth	3 %(w/v)
23368	NaCl		growth	4.5 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23368	64552 ChEBI	2-hydroxybutyrate	+	respiration
23368	16763 ChEBI	2-oxobutanoate	+	respiration
23368	28644 ChEBI	2-oxopentanoate	+	respiration
23368	37054 ChEBI	3-hydroxybutyrate	+	respiration
23368	16724 ChEBI	4-hydroxybutyrate	+	respiration
23368	30089 ChEBI	acetate	+	respiration
23368	17128 ChEBI	adipate	-	carbon source
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
23368	17925 ChEBI	alpha-D-glucose	+	respiration
68368	27613 ChEBI	amygdalin	-	fermentation	from API 20E
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
23368	73706 ChEBI	bromosuccinate	+	respiration
23368	17057 ChEBI	cellobiose	-	respiration
23368	16383 ChEBI	cis-aconitate	+	respiration
23368	16947 ChEBI	citrate	+	carbon source
23368	16947 ChEBI	citrate	+	respiration
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
23368	8391 ChEBI	D-gluconate	+	respiration
23368	17784 ChEBI	D-glucosaminic acid	+	respiration
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68368	17634 ChEBI	D-glucose	-	fermentation	from API 20E
23368	14314 ChEBI	D-glucose 6-phosphate	-	respiration
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68368	16899 ChEBI	D-mannitol	-	fermentation	from API 20E
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
23368	16523 ChEBI	D-serine	-	respiration
23368	27689 ChEBI	decanoate	+	carbon source
68369	27689 ChEBI	decanoate	+	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
23368	15740 ChEBI	formate	+	respiration
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
23368	24265 ChEBI	gluconate	+	carbon source
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
23368	17234 ChEBI	glucose	+	carbon source
23368	32323 ChEBI	glucuronamide	-	respiration
23368	17754 ChEBI	glycerol	+	respiration
23368	28087 ChEBI	glycogen	-	respiration
23368	73804 ChEBI	glycyl L-aspartic acid	-	respiration
23368	73784 ChEBI	glycyl-l-glutamate	-	respiration
23368	21217 ChEBI	L-alaninamide	+	respiration
23368	73786 ChEBI	L-alanylglycine	+	respiration
23368	30849 ChEBI	L-arabinose	-	respiration
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68368	30849 ChEBI	L-arabinose	-	fermentation	from API 20E
23368	17196 ChEBI	L-asparagine	+	respiration
23368	29985 ChEBI	L-glutamate	+	respiration
23368	15971 ChEBI	L-histidine	+	respiration
23368	15603 ChEBI	L-leucine	+	respiration
23368	17295 ChEBI	L-phenylalanine	+	respiration
23368	17203 ChEBI	L-proline	+	respiration
23368	18183 ChEBI	L-pyroglutamic acid	+	respiration
68368	62345 ChEBI	L-rhamnose	-	fermentation	from API 20E
23368	17115 ChEBI	L-serine	+	respiration
23368	16857 ChEBI	L-threonine	+	respiration
23368	24996 ChEBI	lactate	+	respiration
68368	25094 ChEBI	lysine	-	degradation	from API 20E
23368	25115 ChEBI	malate	+	carbon source
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
23368	15792 ChEBI	malonate	-	respiration
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68368	28053 ChEBI	melibiose	-	fermentation	from API 20E
23368	51850 ChEBI	methyl pyruvate	+	respiration
68368	17268 ChEBI	myo-inositol	-	fermentation	from API 20E
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
23368	18401 ChEBI	phenylacetate	+	carbon source
23368	41865 ChEBI	sebacic acid	-	respiration
68368	30911 ChEBI	sorbitol	-	fermentation	from API 20E
23368	17992 ChEBI	sucrose	-	respiration
68368	17992 ChEBI	sucrose	-	fermentation	from API 20E
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
23368	53426 ChEBI	tween 80	+	respiration
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE
68368	16199 ChEBI	urea	+	hydrolysis	from API 20E

Antibiotic resistance

@ref	ChEBI	Metabolite	Is antibiotic	Is resistant	Resistance conc.
23368	27902	tetracycline			30 µg

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
68369	35581 ChEBI	indole	from API 20NE
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	-		from API 20E
68369	35581 ChEBI	indole		-	from API 20NE
68368	35581 ChEBI	indole		-	from API 20E

Enzymes

@ref	Value	Activity	Ec
23368	acid phosphatase	+	3.1.3.2
23368	alkaline phosphatase	+	3.1.3.1
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68368	beta-galactosidase	-	3.2.1.23	from API 20E
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
23368	catalase	+	1.11.1.6
23368	cystine arylamidase	-	3.4.11.3
23368	cytochrome oxidase	+	1.9.3.1
23368	esterase (C 4)	+
23368	esterase lipase (C 8)	-
23368	esterase lipase (C 8)	+
68369	gelatinase	-		from API 20NE
68368	gelatinase	-		from API 20E
23368	leucine arylamidase	+	3.4.11.1
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
23368	naphthol-AS-BI-phosphohydrolase	+
23368	nitrate reductase	-	1.7.99.4
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
23368	urease	+	3.5.1.5
68369	urease	+	3.5.1.5	from API 20NE
68368	urease	+	3.5.1.5	from API 20E
23368	valine arylamidase	-

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
17291	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	+/-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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
17291	-	-	-	-	+	-	-	-	+	-	-	-	-	-	+	+	-	+	+	+	+/-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Laboratory	#Lab enrichment
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
17291	uncultivated field soil	Mugla	Turkey	TUR	Asia
23368	field soil after enrichment with oxalate in mineral medium

Taxonmaps

69479

Global distribution of 16S sequence AB510956 (>99% sequence identity) for Pandoraea from Microbeatlas

Aquatic Samples	4192
Soil Samples	6943
Animal Samples	3605
Plant Samples	5843
Total Samples	20583

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17291	1	Risk group (German 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	ASM93460v2 assembly for Pandoraea vervacti NS15	complete	GCA_000934605	656178.12	2927181219	656178	96.84
66792	Pandoraea vervacti strain NS15	complete		656178.5		656178	94.2

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17291	Pandoraea vervacti gene for 16S rRNA, partial sequence, strain: NS15	AB510956	1378		656178

GC content

@ref	GC-content (mol%)	Method
17291	65.8	thermal denaturation, midpoint method (Tm)
23368	65.8	Thermal denaturation, fluorometry

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pandoraea vervacti NS15
NCBI: GCA_000934605

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	84.90	no
125439	motility	BacteriaNetⓘ	yes	62.50	no
125439	gram_stain	BacteriaNetⓘ	negative	90.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pandoraea vervacti NS15
NCBI: GCA_000934605.2

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	no
125438	anaerobic	anaerobicⓘ	no	97.54	no
125438	aerobic	aerobicⓘ	yes	81.13	no
125438	spore-forming	spore-formingⓘ	no	88.66	no
125438	thermophilic	thermophileⓘ	no	97.98	no
125438	flagellated	motile2+ⓘ	yes	87.63	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Complete genome sequence of oxalate-degrading bacterium Pandoraea vervacti DSM 23571(T).	Ee R, Yong D, Lim YL, Yin WF, Chan KG	J Biotechnol	10.1016/j.jbiotec.2015.03.020	2015
Phylogeny	Pandoraea oxalativorans sp. nov., Pandoraea faecigallinarum sp. nov. and Pandoraea vervacti sp. nov., isolated from oxalate-enriched culture.	Sahin N, Tani A, Kotan R, Sedlacek I, Kimbara K, Tamer AU	Int J Syst Evol Microbiol	10.1099/ijs.0.026138-0	2010

References

#17291	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23571
#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 )
#23368	Nurettin Sahin, Akio Tani, Recep Kotan, Ivo Sedlácek, Kazuhide Kimbara, Abdurrahman U. Tamer: Pandoraea oxalativorans sp. nov., Pandoraea faecigallinarum sp. nov. and Pandoraea vervacti sp. nov., isolated from oxalate-enriched culture. IJSEM 61: 2247 - 2253 2011 ( DOI 10.1099/ijs.0.026138-0 , PubMed 20952546 )
#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) .
#68368	Automatically annotated from API 20E .
#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 .
#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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Pandoraea vervacti (DSM 23571, CCM 7667, NBRC 106088)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API 20E

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000934605

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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