Name: Pandoraea vervacti 561
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2066

Type strain:

Species: Pandoraea vervacti

Strain Designation: 561, NS15

Culture col. no.: DSM 23571, CCM 7667, NBRC 106088

Strain history: <- N. Sahin, Mugla University, Kötekli, Turkey; NS15

NCBI tax ID(s): 656178 (species)

SI-ID 378120

CCM 7667, DSM 23571, NBRC 106088, LMG 28170

Section

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

Gram-negative
motile
rod-shaped
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	*Pandoraea*
	Species	**Pandoraea vervacti**
	Full Scientific Name (LPSN)	Pandoraea vervacti Sahin et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #23368]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.982

[Ref.: #23368]	Cell length	2.8 µm

[Ref.: #23368]	Cell width	0.9 µm

[Ref.: #23368]	Cell shape	rod-shaped

[Ref.: #23368]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %95.793

[Ref.: #23368]	Colony size	1-2 mm
[Ref.: #23368]	Colony color	cream
[Ref.: #23368]	Incubation period	2 days
[Ref.: #23368]	Cultivation medium used	TSA

[Ref.: #17291]	Incubation period	1-2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17291]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #17291]

Culture medium growth

[Ref.: #17291]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17291]

Culture medium composition

expand / minimize

[Ref.: #23368]

Culture medium

Trypticase Soy Agar (TSA)

[Ref.: #23368]

Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #17291]			growth	28 °C
[Ref.: #23368]			growth	30-42 °C

[Ref.: #17291]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.963

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #23368]		NaCl		growth	3	%(w/v)
[Ref.: #23368]		NaCl	no	growth	4.5	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23368]	2-hydroxybutyrate ChEBI	+	respiration
[Ref.: #23368]	2-oxobutanoate ChEBI	+	respiration
[Ref.: #23368]	2-oxopentanoate ChEBI	+	respiration
[Ref.: #23368]	3-hydroxybutyrate ChEBI	+	respiration
[Ref.: #23368]	4-hydroxybutyrate ChEBI	+	respiration
[Ref.: #23368]	acetate ChEBI	+	respiration
[Ref.: #23368]	adipate ChEBI	-	carbon source
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #23368]	alpha-D-glucose ChEBI	+	respiration
[Ref.: #68368]	amygdalin ChEBI	-	fermentation	* from API 20E
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE, API 20E
[Ref.: #23368]	bromosuccinate ChEBI	+	respiration
[Ref.: #23368]	cellobiose ChEBI	-	respiration
[Ref.: #23368]	cis-aconitate ChEBI	+	respiration
[Ref.: #23368]	citrate ChEBI	+	carbon source
[Ref.: #23368]	citrate ChEBI	+	respiration
[Ref.: #68368]	citrate ChEBI	+	assimilation	* from API 20E
[Ref.: #23368]	D-gluconate ChEBI	+	respiration
[Ref.: #23368]	D-glucosaminic acid ChEBI	+	respiration
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE, API 20E
[Ref.: #23368]	D-glucose 6-phosphate ChEBI	-	respiration
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68368]	D-mannitol ChEBI	-	fermentation	* from API 20E
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #23368]	D-serine ChEBI	-	respiration
[Ref.: #23368]	decanoate ChEBI	+	carbon source
[Ref.: #68369]	decanoate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #23368]	formate ChEBI	+	respiration
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE, API 20E
[Ref.: #23368]	gluconate ChEBI	+	carbon source
[Ref.: #68369]	gluconate ChEBI	+	assimilation	* from API 20NE
[Ref.: #23368]	glucose ChEBI	+	carbon source
[Ref.: #23368]	glucuronamide ChEBI	-	respiration
[Ref.: #23368]	glycerol ChEBI	+	respiration
[Ref.: #23368]	glycogen ChEBI	-	respiration
[Ref.: #23368]	glycyl L-aspartic acid ChEBI	-	respiration
[Ref.: #23368]	glycyl-l-glutamate ChEBI	-	respiration
[Ref.: #23368]	L-alaninamide ChEBI	+	respiration
[Ref.: #23368]	L-alanylglycine ChEBI	+	respiration
[Ref.: #23368]	L-arabinose ChEBI	-	respiration
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68368]	L-arabinose ChEBI	-	fermentation	* from API 20E
[Ref.: #23368]	L-asparagine ChEBI	+	respiration
[Ref.: #23368]	L-glutamate ChEBI	+	respiration
[Ref.: #23368]	L-histidine ChEBI	+	respiration
[Ref.: #23368]	L-leucine ChEBI	+	respiration
[Ref.: #23368]	L-phenylalanine ChEBI	+	respiration
[Ref.: #23368]	L-proline ChEBI	+	respiration
[Ref.: #23368]	L-pyroglutamic acid ChEBI	+	respiration
[Ref.: #68368]	L-rhamnose ChEBI	-	fermentation	* from API 20E
[Ref.: #23368]	L-serine ChEBI	+	respiration
[Ref.: #23368]	L-threonine ChEBI	+	respiration
[Ref.: #23368]	lactate ChEBI	+	respiration
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #23368]	malate ChEBI	+	carbon source
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #23368]	malonate ChEBI	-	respiration
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68368]	melibiose ChEBI	-	fermentation	* from API 20E
[Ref.: #23368]	methyl pyruvate ChEBI	+	respiration
[Ref.: #68368]	myo-inositol ChEBI	-	fermentation	* from API 20E
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #23368]	phenylacetate ChEBI	+	carbon source
[Ref.: #23368]	sebacic acid ChEBI	-	respiration
[Ref.: #68368]	sorbitol ChEBI	-	fermentation	* from API 20E
[Ref.: #23368]	sucrose ChEBI	-	respiration
[Ref.: #68368]	sucrose ChEBI	-	fermentation	* from API 20E
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE, API 20E
[Ref.: #23368]	tween 80 ChEBI	+	respiration
[Ref.: #68369]	urea ChEBI	+	hydrolysis	* from API 20NE, API 20E
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Metabolite	Antibiotic resistance	Concentration
[Ref.: #23368]		tetracycline ChEBI	no	30	µg

	Metabolite	Production
[Ref.: #68368]	acetoin ChEBI	no	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68369]	indole ChEBI	no	* from API 20NE, API 20E

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #68368]		acetoin ChEBI	-		* from API 20E
[Ref.: #68369]		indole ChEBI		-	* from API 20NE, API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #23368]	acid phosphatase	+	3.1.3.2
[Ref.: #23368]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE, API 20E
[Ref.: #68368]	beta-galactosidase	-	3.2.1.23	* from API 20E
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #23368]	catalase	+	1.11.1.6
[Ref.: #23368]	cystine arylamidase	-	3.4.11.3
[Ref.: #23368]	cytochrome oxidase	+	1.9.3.1
[Ref.: #23368]	esterase (C 4)	+
[Ref.: #23368]	esterase lipase (C 8)	-
[Ref.: #23368]	esterase lipase (C 8)	+
[Ref.: #68369]	gelatinase	-		* from API 20NE, API 20E
[Ref.: #23368]	leucine arylamidase	+	3.4.11.1
[Ref.: #68368]	lysine decarboxylase	-	4.1.1.18	* from API 20E
[Ref.: #23368]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #23368]	nitrate reductase	-	1.7.99.4
[Ref.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #23368]	urease	+	3.5.1.5
[Ref.: #68369]	urease	+	3.5.1.5	* from API 20NE, API 20E
[Ref.: #23368]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

API® 20E:

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

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #17291]	16848	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	+/-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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.: #17291]	23870	-	-	-	-	+	-	-	-	+	-	-	-	-	-	+	+	-	+	+	+	+/-

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

[Ref.: #17291]	Sample type/isolated from	uncultivated field soil
[Ref.: #17291]	Geographic location (country and/or sea, region)	Mugla
[Ref.: #17291]	Country	Turkey
[Ref.: #17291]	Country ISO 3 Code	TUR
[Ref.: #17291]	Continent	Asia

[Ref.: #23368]	Sample type/isolated from	field soil after enrichment with oxalate in mineral medium
* marker position based on {}

Isolation sources categories

#Engineered	#Laboratory	#Lab enrichment
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #17291]

Biosafety level

Risk group (German classification)
According to TRBA 466

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

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #17291]	Pandoraea vervacti gene for 16S rRNA, partial sequence, strain: NS15	AB510956	1378	ENA	656178 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pandoraea vervacti NS15	GCA_000934605	complete	GenBank	656178 tax ID	*
[Ref.: #66792]	Pandoraea vervacti strain NS15	656178.9	plasmid	PATRIC	656178 tax ID	*
[Ref.: #66792]	Pandoraea vervacti strain NS15	656178.5	complete	PATRIC	656178 tax ID	*
[Ref.: #66792]	Pandoraea vervacti NS15	2927181219	complete	JGI IMG/M	656178 tax ID	*

[Ref.: #17291]	GC-content	65.8 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #23368]	GC-content	65.8 mol%	Thermal denaturation, fluorometry

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: Pandoraea vervacti NS15 NCBI: GCA_000934605.2
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pandoraea vervacti NS15 NCBI: GCA_000934605.1
[Ref.: #69480]	motile	yes	88.68	no
[Ref.: #69480]	flagellated	no	58.531	no
[Ref.: #69480]	gram-positive	no	98.717	no
[Ref.: #69480]	anaerobic	no	98.81	no
[Ref.: #69480]	aerobic	yes	90.975	no
[Ref.: #69480]	halophile	no	94.024	no
[Ref.: #69480]	spore-forming	no	94.044	no
[Ref.: #69480]	glucose-util	yes	64.918	yes
[Ref.: #69480]	thermophile	no	98.902	yes
[Ref.: #69480]	glucose-ferment	no	89.565	yes
[Ref.: #69480]	motile	yes	88.68	no
[Ref.: #69480]	flagellated	no	58.531	no
[Ref.: #69480]	gram-positive	no	98.717	no
[Ref.: #69480]	anaerobic	no	98.81	no
[Ref.: #69480]	aerobic	yes	90.975	no
[Ref.: #69480]	halophile	no	94.024	no
[Ref.: #69480]	spore-forming	no	94.044	no
[Ref.: #69480]	glucose-util	yes	64.918	yes
[Ref.: #69480]	thermophile	no	98.902	yes
[Ref.: #69480]	glucose-ferment	no	89.565	yes

Availability in culture collections External links

[Ref.: #17291]

Culture collection no.

DSM 23571, CCM 7667, NBRC 106088

[Ref.: #71713]

SI-ID 378120

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 .

#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 )

#71713

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-ID378120.1 )

* These data were automatically processed and therefore are not curated

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Pandoraea vervacti NS15

Pandoraea vervacti NS15

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