Pseudoxanthomonas koreensis (KCTC 12208, IAM 15116, CCUG 55488)

Name: Pseudoxanthomonas koreensis (KCTC 12208, IAM 15116, CCUG 55488)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 134100

Type strain

Strain Designation T7-09

Culture col. no. KCTC 12208 IAM 15116 CCUG 55488 CIP 108711 T7-09 3 more

NCBI tax ID(s) 266061

Special Collections CCUG JCM KCTC CIP Literature strains

History <- ST Lee, KAIST CIP <- 2005, IAM <- D.C. Yang, Kyung Hee Univ., Kyunggi, South Korea: strain T7-09

Links

Pseudoxanthomonas koreensis T7-09 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from Soil,ginseng field.

Gram-negative rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 138033

IAM 15116,KCTC 12208,NBRC 101160,DSM 17802,JCM 21576,CIP 108711,CCUG 55488

@ref 20215

Last LPSN update 2026-02-09 11:32:06

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Lysobacteraceae

Genus Pseudoxanthomonas

Species Pseudoxanthomonas koreensis

Full scientific name Pseudoxanthomonas koreensis Yang et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
31284	negative	rod-shaped
67771	negative
125438	negative		97.968
125439	negative		96.4
120484	negative	rod-shaped

Colony morphology

60606

Incubation period1 day

Pigmentation

@ref	Production	Name
120484		Pyocyanin

Culture and growth conditions

Culture medium

@ref	Name	Growth	Composition	Medium link
38294	MEDIUM 328- for nutrient agar		Distilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
120484	CIP Medium 328			Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
31284	positive	growth	30-37	mesophilic
31284	positive	optimum	30	mesophilic
38294	positive	growth	30	mesophilic
60606	positive	growth	30	mesophilic
67771	positive	growth	30	mesophilic
120484	positive	growth	25-37	mesophilic
120484	negative	growth	10

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31284	aerobe
60606	aerobe
67771	aerobe
120484	facultative anaerobe
125439	obligate aerobe	99

Spore formation

@ref	Spore formation	Confidence
31284
125438		94.33
125439		95.7

Halophily

@ref	Salt	Growth	Tested relation	Concentration
120484	NaCl	positive	growth	0-10 %

Observation

67771

Observationquinones: Q-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
120484	16947 ChEBI	citrate	-	carbon source
120484	4853 ChEBI	esculin	+	hydrolysis
120484	17632 ChEBI	nitrate	+	reduction
120484	17632 ChEBI	nitrate	+	respiration
120484	16301 ChEBI	nitrite	+	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
120484	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
120484	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	+	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
120484	amylase	+
68382	beta-galactosidase	+	3.2.1.23	from API zym
120484	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
120484	caseinase	+	3.4.21.50
31284	catalase	+	1.11.1.6
120484	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31284	cytochrome oxidase	+	1.9.3.1
120484	DNase	+
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
120484	gelatinase	+
120484	lecithinase	+
68382	leucine arylamidase	+	3.4.11.1	from API zym
120484	lipase	-
68382	lipase (C 14)	-		from API zym
120484	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
120484	ornithine decarboxylase	-	4.1.1.17
120484	oxidase	-
120484	protease	+
68382	trypsin	+	3.4.21.4	from API zym
120484	tryptophan deaminase	-
120484	tween esterase	-
31284	urease	+	3.5.1.5
120484	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
120484	-	+	+	+	-	+	-	-	+	+	+	+	-	+	-	+	+	+	-	-

API biotype100

@ref	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
120484	not determinedn.d.	+	-	+	+	+	-	+	+	-	+	+	-	-	-	-	+	-	-	+	+	+	-	-	-	-	-	-	-	-	-	-	+	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
60606	Soil,ginseng field	Daejon	Republic of Korea	KOR	Asia
67771	From compost		Republic of Korea	KOR	Asia
120484	Environment, Soil, ginseng field	Daejeon	Republic of Korea	KOR	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
120484	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1009322v1 assembly for Pseudoxanthomonas koreensis KCTC 12208	contig	GCA_010093225	266061.3	2995753857	266061	56.68

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
31284	Pseudoxanthomonas koreensis strain T7-09 16S ribosomal RNA gene, partial sequence	AY550263	1419		266061
124043	Pseudoxanthomonas koreensis gene for 16S rRNA, partial sequence, strain: NBRC 101160.	AB681402	1463		266061

GC content

31284

GC-content (mol%)69.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudoxanthomonas koreensis KCTC 12208
NCBI: GCA_010093225

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.70	no
125439	motility	BacteriaNetⓘ	yes	82.90	no
125439	gram_stain	BacteriaNetⓘ	negative	96.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudoxanthomonas koreensis strain KCTC 12208
PATRIC: 266061.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.97	no
125438	anaerobic	anaerobicⓘ	no	97.61	no
125438	spore-forming	spore-formingⓘ	no	94.33	yes
125438	aerobic	aerobicⓘ	yes	81.96	no
125438	thermophilic	thermophileⓘ	no	94.88	yes
125438	flagellated	motile2+ⓘ	no	68.52	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudoxanthomonas humi sp. nov., a bacterium isolated from rhizospheric soil of Fraxinus chinensis in Gyeonggi Province, South Korea.	Akter S, Jo H, Du J, Won K, Yin CS, Kook M, Yu H, Choi HS, Kim MK, Yi TH	Arch Microbiol	10.1007/s00203-015-1157-5	2015
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

#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 )
#27603	IJSEM 787 2005 ( DOI 10.1099/ijs.0.63210-0 , PubMed 15774663 )
#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
#38294	; Curators of the CIP;
#60606	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 55488
#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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68382	Automatically annotated from API zym .
#120484	Collection of Institut Pasteur ; Curators of the CIP; CIP 108711
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Rate our new design

Content

About us

Pseudoxanthomonas koreensis (KCTC 12208, IAM 15116, CCUG 55488)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_010093225

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media