Name: Pandoraea oxalativorans TA25
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 2063

Type strain:

Species: Pandoraea oxalativorans

Strain Designation: TA25

Culture col. no.: DSM 23570, CCM 7677, NBRC 106091, NEU 105

Strain history: <- N. Sahin, Mugla University, Kötekli, Turkey; TA25 <- A. Ü. Tamer, Celal Bayar University, Turkey

NCBI tax ID(s): 573737 (species)

SI-ID 378119

CCM 7677, DSM 23570, NBRC 106091, LMG 28169

Other strains from Pandoraea oxalativorans

P. oxalativorans TA02, TA2, DSM 23573, CCM 7670, ...
P. oxalativorans TA04, TA4, DSM 23574, CCM 7671, ...

Section

Pandoraea oxalativorans TA25 is a mesophilic, Gram-negative, motile bacterium that was isolated from soil litter close to Oxalis sp..

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 oxalativorans**
	Full Scientific Name (LPSN)	Pandoraea oxalativorans Sahin et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #23368]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.997

[Ref.: #23368]	Cell length	2.3-2.8 µm

[Ref.: #23368]	Cell width	0.7-0.9 µm

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

[Ref.: #23368]	Motility	yes

[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.: #17290]	Incubation period	1-2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17290]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #17290]

Culture medium growth

[Ref.: #17290]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17290]

Culture medium composition

expand / minimize

[Ref.: #23368]

Culture medium

Trypticase Soy Agar (TSA)

[Ref.: #23368]

Culture medium growth

	Kind of temperature		Temperature
[Ref.: #17290]		growth	28 °C
[Ref.: #23368]		growth	30-37 °C
[Ref.: #23368]	no	growth	42 °C

[Ref.: #17290]	Temperature range	mesophilic
[Ref.: #23368]	Temperature range	mesophilic
[Ref.: #23368]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %96
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.996

	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.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #23163]	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.: #23368]	D-gluconate ChEBI	-	respiration
[Ref.: #23368]	D-gluconate ChEBI	+	respiration
[Ref.: #23368]	D-glucosaminic acid ChEBI	-	respiration
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #23368]	D-glucose 6-phosphate ChEBI	-	respiration
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[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
[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.: #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.: #23368]	L-serine ChEBI	+	respiration
[Ref.: #23368]	L-threonine ChEBI	+	respiration
[Ref.: #23368]	lactate ChEBI	+	respiration
[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.: #23368]	methyl pyruvate ChEBI	+	respiration
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #23368]	phenylacetate ChEBI	+	carbon source
[Ref.: #23368]	sebacic acid ChEBI	-	respiration
[Ref.: #23368]	sucrose ChEBI	-	respiration
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #23368]	tween 80 ChEBI	+	respiration
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	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	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	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
[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.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #23368]	leucine arylamidase	+	3.4.11.1
[Ref.: #23368]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #23368]	nitrate reductase	-	1.7.99.4
[Ref.: #23368]	urease	+	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #23368]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

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.: #17290]	23867	-	-	-	-	-	-	-	-	+/-	-	-	-	-	-	-	-	-	+	+	+	+/-

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

[Ref.: #17290]	Sample type/isolated from	soil litter close to Oxalis sp.
[Ref.: #17290]	Host species	Oxalis
[Ref.: #17290]	Geographic location (country and/or sea, region)	Izmir
[Ref.: #17290]	Country	Turkey
[Ref.: #17290]	Country ISO 3 Code	TUR
[Ref.: #17290]	Continent	Asia

[Ref.: #23368]	Sample type/isolated from	soil litter close to oxalate-producing plants of the genera after enrichment with oxalate in mineral medium
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Engineered	#Laboratory	#Lab enrichment
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB469785 (>99% sequence identity) for Pandoraea from Microbeatlas

Aquatic Samples	1255
Soil Samples	2081
Animal Samples	1218
Plant Samples	1157
Total Samples	5711

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

[Ref.: #17290]

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.: #17290]	Pandoraea oxalativorans gene for 16S rRNA, partial sequence, strain: TA25	AB469785	1375	ENA	573737 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pandoraea oxalativorans DSM 23570	GCA_000972785	complete	GenBank	573737 tax ID	*
[Ref.: #66792]	Pandoraea oxalativorans strain DSM 23570	573737.13	plasmid	PATRIC	573737 tax ID	*
[Ref.: #66792]	Pandoraea oxalativorans strain DSM 23570	573737.12	plasmid	PATRIC	573737 tax ID	*
[Ref.: #66792]	Pandoraea oxalativorans strain DSM 23570	573737.10	plasmid	PATRIC	573737 tax ID	*
[Ref.: #66792]	Pandoraea oxalativorans strain DSM 23570	573737.11	plasmid	PATRIC	573737 tax ID	*
[Ref.: #66792]	Pandoraea oxalativorans strain DSM-23570	573737.6	complete	PATRIC	573737 tax ID	*

[Ref.: #17290]	GC-content	62.1 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #23368]	GC-content	62.1 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 oxalativorans DSM 23570 NCBI: GCA_000972785.3
[Ref.: #69481]	spore-forming	no	96	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pandoraea oxalativorans DSM 23570 NCBI: GCA_000972785.1
[Ref.: #69480]	motile	yes	89.413	no
[Ref.: #69480]	flagellated	no	70.249	no
[Ref.: #69480]	gram-positive	no	98.682	yes
[Ref.: #69480]	anaerobic	no	99.107	no
[Ref.: #69480]	aerobic	yes	91.752	no
[Ref.: #69480]	halophile	no	93.816	no
[Ref.: #69480]	spore-forming	no	94.855	no
[Ref.: #69480]	glucose-util	yes	64.337	yes
[Ref.: #69480]	glucose-ferment	no	89.428	yes
[Ref.: #69480]	thermophile	no	99.063	no
[Ref.: #69480]	motile	yes	89.413	no
[Ref.: #69480]	flagellated	no	70.249	no
[Ref.: #69480]	gram-positive	no	98.682	yes
[Ref.: #69480]	anaerobic	no	99.107	no
[Ref.: #69480]	aerobic	yes	91.752	no
[Ref.: #69480]	halophile	no	93.816	no
[Ref.: #69480]	spore-forming	no	94.855	no
[Ref.: #69480]	glucose-util	yes	64.337	yes
[Ref.: #69480]	thermophile	no	99.063	no
[Ref.: #69480]	glucose-ferment	no	89.428	yes
[Ref.: #69480]	motile	yes	89.413	no
[Ref.: #69480]	flagellated	no	70.249	no
[Ref.: #69480]	gram-positive	no	98.682	yes
[Ref.: #69480]	anaerobic	no	99.107	no
[Ref.: #69480]	aerobic	yes	91.752	no
[Ref.: #69480]	halophile	no	93.816	no
[Ref.: #69480]	spore-forming	no	94.855	no
[Ref.: #69480]	glucose-util	yes	64.337	yes
[Ref.: #69480]	thermophile	no	99.063	no
[Ref.: #69480]	glucose-ferment	no	89.428	yes

Availability in culture collections External links

[Ref.: #17290]

Culture collection no.

DSM 23570, CCM 7677, NBRC 106091, NEU 105

[Ref.: #71710]

SI-ID 378119

Literature:

	Title	Authors	Journal	DOI	Year
Genetics	Complete genome sequence of Pandoraea oxalativorans DSM 23570(T), an oxalate metabolizing soil bacterium.	Chan KG, Yong D, Ee R, Lim YL, Yu CY, Tee KK, Yin WF, Ang GY	J Biotechnol	10.1016/j.jbiotec.2015.12.037	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	*
	Characterization and Comparative Overview of Complete Sequences of the First Plasmids of Pandoraea across Clinical and Non-clinical Strains.	Yong D, Tee KK, Yin WF, Chan KG	Front Microbiol	10.3389/fmicb.2016.01606	2016	*

References

#17290

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23570

#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 )

#23163

Martin W. Hahn, Elke Lang, Ulrike Brandt, Heinrich Lünsdorf, Qinglong L. Wu, Erko Stackebrandt: Polynucleobacter cosmopolitanus sp. nov., free-living planktonic bacteria inhabiting freshwater lakes and rivers. IJSEM 60: 166 - 173 2010 ( DOI 10.1099/ijs.0.010595-0 , PubMed 19648339 )

#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) .

#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 )

#71710

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-ID378119.1 )

* These data were automatically processed and therefore are not curated

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Pandoraea oxalativorans DSM 23570

Pandoraea oxalativorans DSM 23570

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