Pigmentiphaga daeguensis (DSM 23373, JCM 14330, KCTC 12838)

Name: Pigmentiphaga daeguensis (DSM 23373, JCM 14330, KCTC 12838)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 360

Type strain

Strain Designation K110

Culture col. no. DSM 23373 JCM 14330 KCTC 12838 CCUG 56486 K110

NCBI tax ID(s) 414049

Special Collections DSMZ CCUG JCM KCTC Literature strains

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Pigmentiphaga daeguensis K110 is an aerobe, mesophilic, Gram-negative prokaryote that forms circular colonies and was isolated from wastewater from a dye works.

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

Name and taxonomic classification

SI-ID 309474

JCM 14330,KCTC 12838,DSM 23373,CCUG 56486

@ref 20215

Last LPSN update 2025-12-16 09:46:50

Domain Pseudomonadati

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Alcaligenaceae

Genus Pigmentiphaga

Species Pigmentiphaga daeguensis

Full scientific name Pigmentiphaga daeguensis Yoon et al. 2007

BacDive ID	Other strains from **Pigmentiphaga daeguensis** (1)	Type strain
359	P. daeguensis ASL-4, DSM 10063

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
23274	negative	0.7-2.5 µm	0.3-0.6 µm	rod-shaped
67771	negative

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
23274	1-2 mm	yellowish white	circular	3 days	TSA

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16713	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)		Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
23274	Trypticase Soy Agar (TSA)

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
16713	positive	growth	28	mesophilic
23274	positive	growth	15-46
23274	negative	growth	10
23274	negative	growth	47
23274	positive	optimum	37	mesophilic
67770	positive	growth	37	mesophilic
67771	positive	growth	37	mesophilic

Culture pH

@ref	Ability	Type	PH
23274	positive	optimum	7.0-8.0
23274	positive	growth	5.0-9.0
23274		growth	4.5
23274		growth	9.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
23274	aerobe
67771	aerobe

Spore formation

23274

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
23274	NaCl	positive	maximum	5 %
23274	NaCl	positive	optimum	0.5 %

Observation

67770

Observationquinones: Q-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23274	16808 ChEBI	2-dehydro-D-gluconate	-	assimilation
23274	17426 ChEBI	5-dehydro-D-gluconate	-	assimilation
23274	17128 ChEBI	adipate	+	assimilation
23274	27613 ChEBI	amygdalin	-	assimilation
23274	17108 ChEBI	D-arabinose	-	assimilation
23274	18333 ChEBI	D-arabitol	-	assimilation
23274	28847 ChEBI	D-fucose	-	assimilation
23274	62318 ChEBI	D-lyxose	-	assimilation
23274	16443 ChEBI	D-tagatose	-	assimilation
23274	27689 ChEBI	decanoate	-	assimilation
23274	17113 ChEBI	erythritol	-	assimilation
23274	4853 ChEBI	esculin	-	assimilation
23274	16813 ChEBI	galactitol	-	assimilation
23274	28066 ChEBI	gentiobiose	-	assimilation
23274	17754 ChEBI	glycerol	-	assimilation
23274	28087 ChEBI	glycogen	-	assimilation
23274	15443 ChEBI	inulin	-	assimilation
23274	18403 ChEBI	L-arabitol	-	assimilation
23274	18287 ChEBI	L-fucose	-	assimilation
23274	65328 ChEBI	L-xylose	-	assimilation
23274	17716 ChEBI	lactose	-	assimilation
23274	25115 ChEBI	malate	+	assimilation
23274	6731 ChEBI	melezitose	-	assimilation
23274	320061 ChEBI	methyl alpha-D-glucopyranoside	-	assimilation
23274	43943 ChEBI	methyl alpha-D-mannoside	-	assimilation
23274	74863 ChEBI	methyl beta-D-xylopyranoside	-	assimilation
23274	18401 ChEBI	phenylacetate	-	assimilation
23274	16634 ChEBI	raffinose	-	assimilation
23274	27922 ChEBI	sorbose	-	assimilation
23274	28017 ChEBI	starch	-	assimilation
23274	32528 ChEBI	turanose	-	assimilation
23274	17151 ChEBI	xylitol	-	assimilation

Antibiotic resistance

@ref	ChEBI	Metabolite	Is antibiotic	Is sensitive
23274	3393	carbenicillin
23274	27902	tetracycline

Enzymes

@ref	Value	Activity	Ec
23274	arginine dihydrolase	+/-	3.5.3.6
23274	lysine decarboxylase	-	4.1.1.18
23274	ornithine decarboxylase	-	4.1.1.17
23274	tryptophan deaminase	-	4.1.99.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Engineered	#Industrial
#Engineered	#Waste

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
16713	wastewater from a dye works	Daegu	Republic of Korea	KOR	Asia
60985	Wastewater from a dye works		Republic of Korea	KOR	Asia
67770	Wastewater from a dye works
67771	From wastewater		Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence EF100696 (>99% sequence identity) for Pigmentiphaga from Microbeatlas

Aquatic Samples	3532
Soil Samples	1825
Animal Samples	1092
Plant Samples	890
Total Samples	7339

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16713	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3952303v1 assembly for Pigmentiphaga daeguensis JCM 14330	scaffold	GCA_039523035	414049	57.04

Genome browser: GCA_039523035

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16713	Pigmentiphaga daeguensis strain K110 16S ribosomal RNA gene, partial sequence	EF100696	1486		414049

GC content

@ref	GC-content (mol%)	Method
16713	67.4	high performance liquid chromatography (HPLC)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pigmentiphaga daeguensis sp. nov., isolated from wastewater of a dye works, and emended description of the genus Pigmentiphaga.	Yoon JH, Kang SJ, Kim W, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.64901-0	2007

References

#16713	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23373
#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 )
#23274	Jung-Hoon Yoon, So-Jung Kang, Wonyong Kim, Tae-Kwang Oh: Pigmentiphaga daeguensis sp. nov., isolated from wastewater of a dye works, and emended description of the genus Pigmentiphaga. IJSEM 57: 1188 - 1191 2007 ( DOI 10.1099/ijs.0.64901-0 , PubMed 17551027 )
#60985	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 56486
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 )

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Pigmentiphaga daeguensis (DSM 23373, JCM 14330, KCTC 12838)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_039523035

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

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