Name: Pseudoxanthomonas daejeonensis TR6-08
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17508

Type strain:

Species: Pseudoxanthomonas daejeonensis

Strain Designation: TR6-08, 49.101

Culture col. no.: CCUG 55487, CIP 108710, DSM 17801, IAM 15115, KCTC 12207, JCM 21575, NBRC 101159

Strain history: CIP <- 2005, IAM <- D.C. Yang, Kyung Hee Univ., Kyungii, South Korea: strain TR6-08

NCBI tax ID(s): 266062 (species)

SI-ID 138032

IAM 15115, KCTC 12207, NBRC 101159, DSM 17801, JCM 21575, CIP 108710, CCUG 55487

Section

Pseudoxanthomonas daejeonensis TR6-08 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from compost near Daejeon city.

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 daejeonensis**
	Full Scientific Name (LPSN)	Pseudoxanthomonas daejeonensis Yang et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #31284]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #118845]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.994

[Ref.: #31284]	Cell shape	rod-shaped
[Ref.: #118845]	Cell shape	rod-shaped

[Ref.: #31284]	Motility	yes
[Ref.: #118845]	Motility	yes

[Ref.: #60605]

Incubation period

2 days

[Ref.: #31284]	Pigment production	yes
[Ref.: #118845]	Pigment production	no
[Ref.: #118845]	Pigment name	Pyocyanin

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7193]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7193]

Culture medium growth

[Ref.: #7193]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7193]

Culture medium composition

expand / minimize

[Ref.: #38293]

Culture medium

MEDIUM 328- for nutrient agar

[Ref.: #38293]

Culture medium growth

[Ref.: #38293]

Culture medium composition

expand / minimize

[Ref.: #118845]

Culture medium

CIP Medium 328

[Ref.: #118845]

Culture medium growth

[Ref.: #118845]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #7193]		growth	30 °C
[Ref.: #31284]		growth	30-37 °C
[Ref.: #31284]		optimum	30 °C
[Ref.: #38293]		growth	30 °C
[Ref.: #60605]		growth	30 °C
[Ref.: #67770]		growth	30 °C
[Ref.: #67771]		growth	30 °C
[Ref.: #118845]		growth	10-30 °C
[Ref.: #118845]	no	growth	37 °C
[Ref.: #118845]	no	growth	41 °C

[Ref.: #7193]	Temperature range	mesophilic
[Ref.: #31284]	Temperature range	mesophilic
[Ref.: #38293]	Temperature range	mesophilic
[Ref.: #60605]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic
[Ref.: #118845]	Temperature range	mesophilic
[Ref.: #118845]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31284]	Oxygen tolerance	aerobe
[Ref.: #60605]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #118845]	Oxygen tolerance	obligate aerobe

[Ref.: #31284]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.988

	Salt	Tested relation		Salt conc.
[Ref.: #118845]	NaCl		growth	0-2	%
[Ref.: #118845]	NaCl	no	growth	4	%
[Ref.: #118845]	NaCl	no	growth	6	%
[Ref.: #118845]	NaCl	no	growth	8	%
[Ref.: #118845]	NaCl	no	growth	10	%

[Ref.: #67770]	Observation	quinones: Q-8
[Ref.: #67771]	Observation	quinones: Q-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31284]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #31284]	alanine ChEBI	+	carbon source
[Ref.: #31284]	arabinose ChEBI	+	carbon source
[Ref.: #118845]	citrate ChEBI	-	carbon source
[Ref.: #31284]	esculin ChEBI	+	hydrolysis
[Ref.: #118845]	esculin ChEBI	+	hydrolysis
[Ref.: #31284]	glucose ChEBI	+	carbon source
[Ref.: #31284]	maltose ChEBI	+	carbon source
[Ref.: #31284]	melibiose ChEBI	+	carbon source
[Ref.: #31284]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #118845]	nitrate ChEBI	+	reduction
[Ref.: #118845]	nitrate ChEBI	-	respiration
[Ref.: #118845]	nitrite ChEBI	-	reduction
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #118845]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite production	Metabolite	Production
[Ref.: #118845]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #118845]	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.: #118845]	amylase	-
[Ref.: #118845]	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.: #118845]	caseinase	-	3.4.21.50
[Ref.: #31284]	catalase	+	1.11.1.6
[Ref.: #118845]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #31284]	cytochrome oxidase	+	1.9.3.1
[Ref.: #118845]	DNase	-
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #118845]	gelatinase	-
[Ref.: #118845]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #118845]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #118845]	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.: #118845]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #118845]	oxidase	+
[Ref.: #118845]	protease	-
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #118845]	tryptophan deaminase	-
[Ref.: #118845]	tween esterase	-
[Ref.: #118845]	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.: #118845]	2882	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.: #118845]	11404	-	+	+	+	-	+	-	-	+	+	+	+	-	+	-	-	-	+	-	-

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

[Ref.: #7193]	Sample type/isolated from	compost near Daejeon city
[Ref.: #7193]	Country	Republic of Korea
[Ref.: #7193]	Country ISO 3 Code	KOR
[Ref.: #7193]	Continent	Asia

[Ref.: #60605]	Sample type/isolated from	Soil,ginseng field
[Ref.: #60605]	Geographic location (country and/or sea, region)	Daejon
[Ref.: #60605]	Country	Republic of Korea
[Ref.: #60605]	Country ISO 3 Code	KOR
[Ref.: #60605]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil of ginseng field

[Ref.: #67771]	Sample type/isolated from	From compost
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia

[Ref.: #118845]	Sample type/isolated from	Environment, Soil, ginseng field
[Ref.: #118845]	Geographic location (country and/or sea, region)	Daejeon
[Ref.: #118845]	Country	Republic of Korea
[Ref.: #118845]	Country ISO 3 Code	KOR
[Ref.: #118845]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered

#Biodegradation

#Composting

What are isolation sources categories?

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

[Ref.: #7193]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118845]	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.: #7193]	Pseudoxanthomonas daejeonensis strain TR6-08 16S ribosomal RNA gene, partial sequence	AY550264	1462	ENA	266062 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Pseudoxanthomonas daejeonensis DSM 17801	GCA_010093205	contig	GenBank	266062 tax ID
[Ref.: #66792]	Pseudoxanthomonas daejeonensis strain DSM 17801	266062.3	wgs	PATRIC	266062 tax ID	*

[Ref.: #31284]	GC-content	68.7 mol%
[Ref.: #67770]	GC-content	68.7 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 daejeonensis strain DSM 17801 PATRIC: 266062.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudoxanthomonas daejeonensis strain DSM 17801 PATRIC: 266062.3
[Ref.: #69480]	motile	yes	87.413	yes
[Ref.: #69480]	gram-positive	no	98.852	yes
[Ref.: #69480]	anaerobic	no	98.898	no
[Ref.: #69480]	aerobic	yes	95.003	yes
[Ref.: #69480]	halophile	no	95.187	no
[Ref.: #69480]	spore-forming	no	95.969	no
[Ref.: #69480]	glucose-util	yes	90.869	no
[Ref.: #69480]	flagellated	no	83.868	no
[Ref.: #69480]	thermophile	no	97.095	yes
[Ref.: #69480]	glucose-ferment	no	90.356	no

Availability in culture collections External links

[Ref.: #7193]

Culture collection no.

CCUG 55487, CIP 108710, DSM 17801, IAM 15115, KCTC 12207, JCM 21575, NBRC 101159

[Ref.: #86505]

SI-ID 138032

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudoxanthomonas helianthi sp. nov., isolated from roots of Jerusalem artichoke (Helianthus tuberosus).	Kittiwongwattana C, Thawai C	Int J Syst Evol Microbiol	10.1099/ijsem.0.001465	2016	*
Phylogeny	Pseudoxanthomonas sangjuensis sp. nov., isolated from greenhouse soil.	Kim SJ, Ahn JH, Weon HY, Lim JM, Kim SG, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijsem.0.000395	2015	*
Phylogeny	Pseudoxanthomonas icgebensis sp. nov., isolated from the midgut of Anopheles stephensi field-collected larvae.	Rani A, Sharma A, Adak T, Bhatnagar RK	J Microbiol	10.1007/s12275-010-0125-7	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	*

References

#7193

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17801

#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 )

#31284

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 #27603 (see below)

#38293 ; Curators of the CIP;
#60605 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 55487

#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;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#68382

Automatically annotated from API zym .

#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 )

#86505

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-ID138032.1 )

#118845 Collection of Institut Pasteur ; Curators of the CIP; CIP 108710

#27603

IJSEM 787 2005 ( DOI 10.1099/ijs.0.63210-0 , PubMed 15774663 )

* These data were automatically processed and therefore are not curated

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Pseudoxanthomonas daejeonensis strain DSM 17801

Pseudoxanthomonas daejeonensis strain DSM 17801

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