Name: Pseudoxanthomonas spadix CIP 109720
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17512

Type strain:

Species: Pseudoxanthomonas spadix

Culture col. no.: CIP 109720, DSM 18855, CCUG 53828, IMMIB AFH-5

Strain history: CIP <- 2007, CCUG <- 2006, A.F. Yassin, Bonn Univ., Bonn, Germany: strain: IMMIB AFH-5

NCBI tax ID(s): 415229 (species)

SI-ID 309496

CCUG 53828, DSM 18855, CIP 109720

Other strains from Pseudoxanthomonas spadix

P. spadix BD-a59, DSM 19372

Section

Pseudoxanthomonas spadix CIP 109720 is a microaerophile, mesophilic, Gram-negative bacterium that was isolated from oil contaminated soil.

Gram-negative
motile
rod-shaped
mesophilic
microaerophile
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	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Lysobacteraceae*
	Genus	*Pseudoxanthomonas*
	Species	**Pseudoxanthomonas spadix**
	Full Scientific Name (LPSN)	Pseudoxanthomonas spadix Young et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #32159]	Gram stain	negative
[Ref.: #122687]	Gram stain	negative

[Ref.: #32159]	Cell shape	rod-shaped
[Ref.: #122687]	Cell shape	rod-shaped

[Ref.: #32159]	Motility	yes
[Ref.: #122687]	Motility	no

[Ref.: #32159]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7745]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7745]

Culture medium growth

[Ref.: #7745]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7745]

Culture medium composition

expand / minimize

[Ref.: #33321]

Culture medium

MEDIUM 10 - Chocolate medium for Actinobacillus pleuropneumoniae, Capnocytophaga cynodegmi, Haemophilus and Neisseria

[Ref.: #33321]

Culture medium growth

[Ref.: #33321]

Culture medium composition

expand / minimize

[Ref.: #122687]

Culture medium

CIP Medium 72

[Ref.: #122687]

Culture medium growth

[Ref.: #122687]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #122687]

Culture medium

CIP Medium 10

[Ref.: #122687]

Culture medium growth

[Ref.: #122687]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #7745]	growth	35 °C
[Ref.: #32159]	growth	22-37 °C
[Ref.: #32159]	optimum	29.5 °C
[Ref.: #33321]	growth	30 °C
[Ref.: #60026]	growth	22-37 °C

[Ref.: #7745]	Temperature range	mesophilic
[Ref.: #32159]	Temperature range	mesophilic
[Ref.: #33321]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7745]	Oxygen tolerance	microaerophile
[Ref.: #32159]	Oxygen tolerance	aerobe
[Ref.: #60026]	Oxygen tolerance	aerobe
[Ref.: #122687]	Oxygen tolerance	obligate aerobe

[Ref.: #32159]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32159]		NaCl		growth	0.5-3	%
[Ref.: #32159]		NaCl		optimum	2	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #32159]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #32159]	glucose ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #122687]	nitrate ChEBI	-	reduction
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #122687]	nitrite ChEBI	-	reduction
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #122687]		indole ChEBI	no
[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.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #32159]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #32159]	catalase	+	1.11.1.6
[Ref.: #122687]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #32159]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #32159]	gelatinase	+
[Ref.: #68369]	gelatinase	+		* from API 20NE
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #122687]	oxidase	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #122687]	urease	-	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #68382]	valine arylamidase	+		* from API zym
	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.: #7745]	24740	-	-	-	-	-	+	+	-	+	-	-	-	-	-	-	-	-	-	-	-	+

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #122687]	12060	-	+	+	+	-	+	+	-	+	-	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #7745]	Sample type/isolated from	oil contaminated soil
[Ref.: #7745]	Geographic location (country and/or sea, region)	Chyai County
[Ref.: #7745]	Country	Taiwan
[Ref.: #7745]	Country ISO 3 Code	TWN
[Ref.: #7745]	Continent	Asia

[Ref.: #60026]	Sample type/isolated from	Soil,oil contaminated sample
[Ref.: #60026]	Geographic location (country and/or sea, region)	Chyai County
[Ref.: #60026]	Country	Taiwan
[Ref.: #60026]	Country ISO 3 Code	TWN
[Ref.: #60026]	Continent	Asia

[Ref.: #122687]	Sample type/isolated from	Environment, Soil, oil contaminated sample
[Ref.: #122687]	Geographic location (country and/or sea, region)	Chyai county
[Ref.: #122687]	Country	Taiwan
[Ref.: #122687]	Country ISO 3 Code	TWN
[Ref.: #122687]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	#Oil (Fuel)
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AM418384 (>99% sequence identity) for Xanthomonas from Microbeatlas

Aquatic Samples	813
Soil Samples	806
Animal Samples	1058
Plant Samples	472
Total Samples	3149

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

[Ref.: #7745]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122687]	Biosafety level	1	Risk group (French classification)

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.: #7745]	Pseudoxanthomonas spadix partial 16S rRNA gene, strain IMMIB AFH-5	AM418384	1521	ENA	415229 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudoxanthomonas spadix DSM 18855	GCA_003703395	contig	GenBank	415229 tax ID	*
[Ref.: #66792]	Pseudoxanthomonas spadix strain DSM 18855	415229.5	wgs	PATRIC	415229 tax ID	*

[Ref.: #32159]

GC-content

68.5 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudoxanthomonas spadix strain DSM 18855 PATRIC: 415229.5
[Ref.: #69480]	gram-positive	no	98.331	no
[Ref.: #69480]	anaerobic	no	98.931	no
[Ref.: #69480]	halophile	no	95.408	no
[Ref.: #69480]	spore-forming	no	95.967	no
[Ref.: #69480]	glucose-util	yes	88.48	yes
[Ref.: #69480]	aerobic	yes	89.836	no
[Ref.: #69480]	flagellated	no	83.256	no
[Ref.: #69480]	thermophile	no	94	yes
[Ref.: #69480]	motile	yes	85.788	yes
[Ref.: #69480]	glucose-ferment	no	92.023	yes

Availability in culture collections External links

[Ref.: #7745]

Culture collection no.

CIP 109720, DSM 18855, CCUG 53828, IMMIB AFH-5

[Ref.: #86509]

SI-ID 309496

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudoxanthomonas winnipegensis sp. nov., derived from human clinical materials and recovered from cystic fibrosis and other patient types in Canada, and emendation of Pseudoxanthomonas spadix Young et al. 2007.	Bernard KA, Vachon A, Pacheco AL, Burdz T, Wiebe D, Beniac DR, Hiebert SL, Booth T, Doyle DA, Lawson P, Bernier AM	Int J Syst Evol Microbiol	10.1099/ijsem.0.004533	2020	*
Phylogeny	Pseudoxanthomonas spadix sp. nov., isolated from oil-contaminated soil.	Young CC, Ho MJ, Arun AB, Chen WM, Lai WA, Shen FT, Rekha PD, Yassin AF	Int J Syst Evol Microbiol	10.1099/ijs.0.65053-0	2007	*

References

#7745

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18855

#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 )

#32159

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28402 (see below)

#33321 ; Curators of the CIP;
#60026 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 53828

#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 .

#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) .

#86509

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-ID309496.1 )

#122687 Collection of Institut Pasteur ; Curators of the CIP; CIP 109720

#28402

IJSEM 1823 2007 ( DOI 10.1099/ijs.0.65053-0 , PubMed 17684265 )

* These data were automatically processed and therefore are not curated

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Pseudoxanthomonas spadix strain DSM 18855

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