Name: Pseudoxanthomonas japonensis 12-3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17505

Type strain:

Species: Pseudoxanthomonas japonensis

Strain Designation: 12-3

Culture col. no.: DSM 17109, CCUG 48231, CIP 107388, JCM 11525, AJ 13070

Strain history: CIP <- 2002, H. Macarie, IRD, Marseille, France: strain 12-3 <- Takashi Iizuka, Ajonomoto Co., Japan

NCBI tax ID(s): 69284 (species)

SI-ID 134448

CCUG 48231, CIP 107388, JCM 11525, DSM 17109, NBRC 101033

Other strains from Pseudoxanthomonas japonensis

P. japonensis CCUG 19935, LMG 9556

Section

Pseudoxanthomonas japonensis 12-3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from polluted urban soil.

Gram-negative
motile
rod-shaped
aerobe
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	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Lysobacteraceae*
	Genus	*Pseudoxanthomonas*
	Species	**Pseudoxanthomonas japonensis**
	Full Scientific Name (LPSN)	Pseudoxanthomonas japonensis Thierry et al. 2004

Information on morphological and physiological properties Morphology

[Ref.: #29999]	Gram stain	negative
[Ref.: #120311]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.988

[Ref.: #29999]	Cell length	1.2 µm

[Ref.: #29999]	Cell width	0.6 µm

[Ref.: #29999]	Cell shape	rod-shaped
[Ref.: #120311]	Cell shape	rod-shaped

[Ref.: #29999]	Motility	yes
[Ref.: #120311]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %97.1

[Ref.: #120311]	Pigment production	no
[Ref.: #120311]	Pigment name	Pyocyanin

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6763]

Culture medium

CASO AGAR (MERCK 105458) (DSMZ Medium 220)

[Ref.: #6763]

Culture medium growth

[Ref.: #6763]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6763]

Culture medium composition

expand / minimize

[Ref.: #38171]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #38171]

Culture medium growth

[Ref.: #38171]

Culture medium composition

expand / minimize

[Ref.: #120311]

Culture medium

CIP Medium 72

[Ref.: #120311]

Culture medium growth

[Ref.: #120311]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #6763]		growth	30 °C
[Ref.: #29999]		growth	10-37 °C
[Ref.: #29999]		optimum	33.5 °C
[Ref.: #38171]		growth	30 °C
[Ref.: #67770]		growth	30 °C
[Ref.: #120311]		growth	25-37 °C
[Ref.: #120311]	no	growth	10 °C
[Ref.: #120311]	no	growth	41 °C

[Ref.: #6763]	Temperature range	mesophilic
[Ref.: #29999]	Temperature range	mesophilic
[Ref.: #38171]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #120311]	Temperature range	mesophilic
[Ref.: #120311]	Temperature range	psychrophilic
[Ref.: #120311]	Temperature range	thermophilic

	pH	Kind of pH		pH
[Ref.: #29999]			optimum	8
[Ref.: #29999]			growth	6.2-9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29999]	Oxygen tolerance	aerobe
[Ref.: #120311]	Oxygen tolerance	obligate aerobe

[Ref.: #29999]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %98
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.995

	Salt	Tested relation		Salt conc.
[Ref.: #29999]	NaCl		growth	0-3	%
[Ref.: #120311]	NaCl		growth	0-2	%
[Ref.: #120311]	NaCl	no	growth	4	%
[Ref.: #120311]	NaCl	no	growth	6	%
[Ref.: #120311]	NaCl	no	growth	8	%
[Ref.: #120311]	NaCl	no	growth	10	%

[Ref.: #67770]

Observation

quinones: Q-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29999]	aspartate ChEBI	+	carbon source
[Ref.: #29999]	cellobiose ChEBI	+	carbon source
[Ref.: #29999]	esculin ChEBI	+	hydrolysis
[Ref.: #120311]	esculin ChEBI	+	hydrolysis
[Ref.: #29999]	galactose ChEBI	+	carbon source
[Ref.: #29999]	glucose ChEBI	+	carbon source
[Ref.: #29999]	glutamate ChEBI	+	carbon source
[Ref.: #29999]	histidine ChEBI	+	carbon source
[Ref.: #29999]	maltose ChEBI	+	carbon source
[Ref.: #120311]	nitrate ChEBI	-	reduction
[Ref.: #120311]	nitrate ChEBI	-	respiration
[Ref.: #120311]	nitrite ChEBI	+	reduction
[Ref.: #29999]	serine ChEBI	+	carbon source
[Ref.: #29999]	trehalose ChEBI	+	carbon source
[Ref.: #29999]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #120311]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite production	Metabolite	Production
[Ref.: #120311]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #120311]	alcohol dehydrogenase	-	1.1.1.1
[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.: #120311]	amylase	-
[Ref.: #120311]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	+	3.2.1.31	* from API zym
[Ref.: #120311]	caseinase	+	3.4.21.50
[Ref.: #29999]	catalase	+	1.11.1.6
[Ref.: #120311]	catalase	-	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #29999]	cytochrome oxidase	+	1.9.3.1
[Ref.: #120311]	DNase	+
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #120311]	gelatinase	+
[Ref.: #120311]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #120311]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #120311]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #120311]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #120311]	oxidase	-
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #120311]	tryptophan deaminase	-
[Ref.: #120311]	tween esterase	+
[Ref.: #120311]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Biotype100:

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

	API ID	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
[Ref.: #120311]	2189	not determinedn.d.	+	-	+	+	-	-	-	-	-	+	+	-	+	-	-	+	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	+	-	-	+	-	-	+	-	-	-	-	-	-	-	+	-	+	-	-	-	+	+	-	-	-	-	-	+	-	+	+	+	-	-	-	+	-	+	+	-

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.: #120311]	10318	-	+	+	+	-	+	-	-	+	+	-	+	-	-	+	-	+	-	-	-

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

[Ref.: #6763]	Sample type/isolated from	polluted urban soil
[Ref.: #6763]	Geographic location (country and/or sea, region)	Tokyo area
[Ref.: #6763]	Country	Japan
[Ref.: #6763]	Country ISO 3 Code	JPN
[Ref.: #6763]	Continent	Asia

[Ref.: #58048]	Sample type/isolated from	Soil,urban,polluted
[Ref.: #58048]	Country	Japan
[Ref.: #58048]	Country ISO 3 Code	JPN
[Ref.: #58048]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Polluted urban soil, collected at the riverside of the Tamagawa River
[Ref.: #67770]	Geographic location (country and/or sea, region)	Tokyo metropolitan area
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia

[Ref.: #120311]	Sample type/isolated from	Environment, Polluted urban soil
[Ref.: #120311]	Geographic location (country and/or sea, region)	Tokyo
[Ref.: #120311]	Country	Japan
[Ref.: #120311]	Country ISO 3 Code	JPN
[Ref.: #120311]	Continent	Asia
[Ref.: #120311]	Isolation date	1994
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	-
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB008507 (>99% sequence identity) for Pseudoxanthomonas from Microbeatlas

Aquatic Samples	7508
Soil Samples	5760
Animal Samples	5790
Plant Samples	1658
Total Samples	20716

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

[Ref.: #6763]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120311]	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.: #6763]	Pseudoxanthomonas japonensis gene for 16S rRNA, partial sequence, strain: 12-3	AB008507	1464	ENA	69284 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Pseudoxanthomonas japonensis DSM 17109	GCA_010093445	contig	GenBank	69284 tax ID
[Ref.: #66792]	Pseudoxanthomonas japonensis strain DSM 17109	69284.4	wgs	PATRIC	69284 tax ID	*

[Ref.: #29999]	GC-content	65.2 mol%
[Ref.: #67770]	GC-content	64.2-66.2 mol%	high performance liquid chromatography (HPLC)

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: Pseudoxanthomonas japonensis strain DSM 17109 PATRIC: 69284.6
[Ref.: #69481]	spore-forming	no	98	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudoxanthomonas japonensis strain DSM 17109 PATRIC: 69284.4
[Ref.: #69480]	gram-positive	no	98.691	no
[Ref.: #69480]	anaerobic	no	97.998	yes
[Ref.: #69480]	halophile	no	95.943	no
[Ref.: #69480]	spore-forming	no	96.001	yes
[Ref.: #69480]	glucose-util	yes	91.073	yes
[Ref.: #69480]	thermophile	no	99.143	yes
[Ref.: #69480]	flagellated	no	79.842	no
[Ref.: #69480]	aerobic	yes	94.299	no
[Ref.: #69480]	glucose-ferment	no	90.729	no
[Ref.: #69480]	motile	yes	88.057	yes

Availability in culture collections External links

[Ref.: #6763]

Culture collection no.

DSM 17109, CCUG 48231, CIP 107388, JCM 11525, AJ 13070

[Ref.: #86502]

SI-ID 134448

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudoxanthomonas putridarboris sp. nov. isolated from rotten tree.	Lee JK, Oh JS, Cho WD, Roh DH	Int J Syst Evol Microbiol	10.1099/ijsem.0.001867	2017	*
Phylogeny	Pseudoxanthomonas indica sp. nov., isolated from a hexachlorocyclohexane dumpsite.	Kumari K, Sharma P, Tyagi K, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.017624-0	2010	*
Phylogeny	Pseudoxanthomonas koreensis sp. nov. and Pseudoxanthomonas daejeonensis sp. nov.	Yang DC, Im WT, Kim MK, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.63210-0	2005	*
Phylogeny	Pseudoxanthomonas mexicana sp. nov. and Pseudoxanthomonas japonensis sp. nov., isolated from diverse environments, and emended descriptions of the genus Pseudoxanthomonas Finkmann et al. 2000 and of its type species.	Thierry S, Macarie H, Iizuka T, Geissdorfer W, Assih EA, Spanevello M, Verhe F, Thomas P, Fudou R, Monroy O, Labat M, Ouattara AS	Int J Syst Evol Microbiol	10.1099/ijs.0.02810-0	2004	*

References

#6763

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17109

#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 )

#29999

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 #26364 (see below)

#38171 ; Curators of the CIP;
#58048 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 48231

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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) .

#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 )

#86502

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-ID134448.1 )

#120311 Collection of Institut Pasteur ; Curators of the CIP; CIP 107388

#26364

IJSEM 2245 2004 ( DOI 10.1099/ijs.0.02810-0 , PubMed 15545466 )

* These data were automatically processed and therefore are not curated

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Pseudoxanthomonas japonensis strain DSM 17109

Pseudoxanthomonas japonensis strain DSM 17109

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