Name: Pigmentiphaga daeguensis K110
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 360

Type strain:

Species: Pigmentiphaga daeguensis

Strain Designation: K110

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

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 414049 (species)

SI-ID 309474

JCM 14330, KCTC 12838, DSM 23373, CCUG 56486

Special Collections

Other strains from Pigmentiphaga daeguensis

Section

When using BacDive for research please cite our paper

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Alcaligenaceae*
	Genus	*Pigmentiphaga*
	Species	**Pigmentiphaga daeguensis**
	Full Scientific Name (LPSN)	Pigmentiphaga daeguensis Yoon et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #23274]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative

[Ref.: #23274]	Cell length	0.7-2.5 µm

[Ref.: #23274]	Cell width	0.3-0.6 µm

[Ref.: #23274]	Cell shape	rod-shaped

[Ref.: #23274]	Motility	no

[Ref.: #23274]	Colony size	1-2 mm
[Ref.: #23274]	Colony color	yellowish white
[Ref.: #23274]	Colony shape	circular
[Ref.: #23274]	Incubation period	3 days
[Ref.: #23274]	Cultivation medium used	TSA

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16713]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #16713]

Culture medium growth

[Ref.: #16713]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16713]

Culture medium composition

expand / minimize

[Ref.: #23274]

Culture medium

Trypticase Soy Agar (TSA)

[Ref.: #23274]

Culture medium growth

	Kind of temperature		Temperature
[Ref.: #16713]		growth	28 °C
[Ref.: #23274]		growth	15-46 °C
[Ref.: #23274]	negative	growth	10 °C
[Ref.: #23274]	negative	growth	47 °C
[Ref.: #23274]		optimum	37 °C
[Ref.: #67770]		growth	37 °C
[Ref.: #67771]		growth	37 °C

	Kind of pH		pH
[Ref.: #23274]		optimum	7.0-8.0
[Ref.: #23274]		growth	5.0-9.0
[Ref.: #23274]	no	growth	4.5
[Ref.: #23274]	no	growth	9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #23274]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #23274]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #23274]		NaCl		maximum	5	%
[Ref.: #23274]		NaCl		optimum	0.5	%

[Ref.: #67770]

Observation

quinones: Q-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23274]	2-dehydro-D-gluconate ChEBI	-	assimilation
[Ref.: #23274]	5-dehydro-D-gluconate ChEBI	-	assimilation
[Ref.: #23274]	adipate ChEBI	+	assimilation
[Ref.: #23274]	amygdalin ChEBI	-	assimilation
[Ref.: #23274]	D-arabinose ChEBI	-	assimilation
[Ref.: #23274]	D-arabitol ChEBI	-	assimilation
[Ref.: #23274]	D-fucose ChEBI	-	assimilation
[Ref.: #23274]	D-lyxose ChEBI	-	assimilation
[Ref.: #23274]	D-tagatose ChEBI	-	assimilation
[Ref.: #23274]	decanoate ChEBI	-	assimilation
[Ref.: #23274]	erythritol ChEBI	-	assimilation
[Ref.: #23274]	esculin ChEBI	-	assimilation
[Ref.: #23274]	galactitol ChEBI	-	assimilation
[Ref.: #23274]	gentiobiose ChEBI	-	assimilation
[Ref.: #23274]	glycerol ChEBI	-	assimilation
[Ref.: #23274]	glycogen ChEBI	-	assimilation
[Ref.: #23274]	inulin ChEBI	-	assimilation
[Ref.: #23274]	L-arabitol ChEBI	-	assimilation
[Ref.: #23274]	L-fucose ChEBI	-	assimilation
[Ref.: #23274]	L-xylose ChEBI	-	assimilation
[Ref.: #23274]	lactose ChEBI	-	assimilation
[Ref.: #23274]	malate ChEBI	+	assimilation
[Ref.: #23274]	melezitose ChEBI	-	assimilation
[Ref.: #23274]	methyl alpha-D-glucopyranoside ChEBI	-	assimilation
[Ref.: #23274]	methyl alpha-D-mannoside ChEBI	-	assimilation
[Ref.: #23274]	methyl beta-D-xylopyranoside ChEBI	-	assimilation
[Ref.: #23274]	phenylacetate ChEBI	-	assimilation
[Ref.: #23274]	raffinose ChEBI	-	assimilation
[Ref.: #23274]	sorbose ChEBI	-	assimilation
[Ref.: #23274]	starch ChEBI	-	assimilation
[Ref.: #23274]	turanose ChEBI	-	assimilation
[Ref.: #23274]	xylitol ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #23274]		carbenicillin ChEBI	yes
[Ref.: #23274]		tetracycline ChEBI		yes

	Enzyme	Enzyme activity	EC number
[Ref.: #23274]	arginine dihydrolase	+/-	3.5.3.6
[Ref.: #23274]	lysine decarboxylase	-	4.1.1.18
[Ref.: #23274]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #23274]	tryptophan deaminase	-	4.1.99.1

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

[Ref.: #16713]	Sample type/isolated from	wastewater from a dye works
[Ref.: #16713]	Geographic location (country and/or sea, region)	Daegu
[Ref.: #16713]	Country	Republic of Korea
[Ref.: #16713]	Country ISO 3 Code	KOR
[Ref.: #16713]	Continent	Asia

[Ref.: #60985]	Sample type/isolated from	Wastewater from a dye works
[Ref.: #60985]	Country	Republic of Korea
[Ref.: #60985]	Country ISO 3 Code	KOR
[Ref.: #60985]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Wastewater from a dye works

[Ref.: #67771]	Sample type/isolated from	From wastewater
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	-
#Engineered	#Waste	#Wastewater

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #16713]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #16713]	Pigmentiphaga daeguensis strain K110 16S ribosomal RNA gene, partial sequence	EF100696	1486	GenBank ENA	414049 tax ID

[Ref.: #16713]

GC-content

67.4 mol%

high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #16713]

Culture collection no.

DSM 23373, JCM 14330, KCTC 12838, CCUG 56486

[Ref.: #70040]

SI-ID 309474

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 .

#70040

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-ID309474.1 )

* These data were automatically processed and therefore are not curated

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