Name: Pedobacter koreensis WPCB189
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 134279

Type strain:

Species: Pedobacter koreensis

Strain Designation: WPCB189

Culture col. no.: KCTC 125365, NBRC 101153, CIP 109707, KCTC 12536

Strain history: CIP <- 2007, NBRC <- J. Chun, Seoul Univ., Seoul, Korea: strain WPCB189

NCBI tax ID(s): 564835 (species)

SI-ID 309552

KCTC 12536, NBRC 101153, CIP 109707

Special Collections

Section

When using BacDive for research please cite our paper

Pedobacter koreensis WPCB189 is an aerobe, Gram-negative, motile bacterium that was isolated from Environment, Fresh water.

Gram-negative
motile
rod-shaped
aerobe
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	*Bacteroidota*
	Class	*Sphingobacteriia*
	Order	*Sphingobacteriales*
	Family	*Sphingobacteriaceae*
	Genus	*Pedobacter*
	Species	**Pedobacter koreensis**
	Full Scientific Name (LPSN)	Pedobacter koreensis Baik et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #32247]	Gram stain	negative
[Ref.: #120482]	Gram stain	negative

[Ref.: #32247]	Cell shape	rod-shaped
[Ref.: #120482]	Cell shape	rod-shaped

[Ref.: #32247]	Motility	yes
[Ref.: #120482]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #37818]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #37818]

Culture medium growth

[Ref.: #37818]

Culture medium composition

expand / minimize

[Ref.: #120482]

Culture medium

CIP Medium 72

[Ref.: #120482]

Culture medium growth

[Ref.: #120482]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #32247]	growth	04-37 °C
[Ref.: #32247]	optimum	25 °C
[Ref.: #37818]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #32247]			optimum	7
[Ref.: #32247]			growth	06-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32247]	Oxygen tolerance	aerobe
[Ref.: #120482]	Oxygen tolerance	obligate aerobe

[Ref.: #32247]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32247]		NaCl		growth	0-2	%

[Ref.: #32247]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32247]	arabinose ChEBI	+	carbon source
[Ref.: #68371]	arbutin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	cellobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32247]	esculin ChEBI	+	hydrolysis
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32247]	galactose ChEBI	+	carbon source
[Ref.: #68371]	gentiobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32247]	glucose ChEBI	+	carbon source
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32247]	glycogen ChEBI	+	carbon source
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32247]	lactose ChEBI	+	carbon source
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32247]	maltose ChEBI	+	carbon source
[Ref.: #32247]	mannose ChEBI	+	carbon source
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32247]	melibiose ChEBI	+	carbon source
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	N-acetylglucosamine ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #120482]	nitrate ChEBI	-	reduction
[Ref.: #120482]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32247]	ribose ChEBI	+	carbon source
[Ref.: #68371]	salicin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	trehalose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32247]	xylitol ChEBI	+	carbon source
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #32247]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #120482]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #32247]	acid phosphatase	+	3.1.3.2
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #32247]	alkaline phosphatase	+	3.1.3.1
[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.: #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.: #32247]	catalase	+	1.11.1.6
[Ref.: #120482]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #32247]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #120482]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #120482]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

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

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #120482]	11635	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.: #120482]	12050	-	+	+	+	-	+	-	-	-	-	+	+	-	+	-	+	+	+	-	-

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

[Ref.: #120482]	Sample type/isolated from	Environment, Fresh water
[Ref.: #120482]	Geographic location (country and/or sea, region)	Woopo Wetland
[Ref.: #120482]	Country	Republic of Korea
[Ref.: #120482]	Country ISO 3 Code	KOR
[Ref.: #120482]	Continent	Asia
[Ref.: #120482]	Isolation date	2000
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence DQ092871 (>99% sequence identity) for Pedobacter koreensis subclade from Microbeatlas

Aquatic Samples	110
Soil Samples	70
Animal Samples	79
Plant Samples	78
Total Samples	337

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

[Ref.: #120482]

Biosafety level

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.: #32247]	Pedobacter koreensis strain WPCB189 16S ribosomal RNA gene, partial sequence	DQ092871	1406	GenBank ENA	564835 tax ID
[Ref.: #124043]	Pedobacter koreensis gene for 16S rRNA, partial sequence, strain: NBRC 101153.	AB681397	1445	GenBank ENA	564835 tax ID	*

[Ref.: #32247]

GC-content

38 mol%

Availability in culture collections External links

[Ref.: #32247]

Culture collection no.

KCTC 125365, NBRC 101153, CIP 109707, KCTC 12536

[Ref.: #91865]

SI-ID 309552

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pedobacter namyangjuensis sp. nov. isolated from soil and reclassification of Nubsella zeaxanthinifaciens Asker et al. 2008 as Pedobacter zeaxanthinifaciens comb. nov.	Kim DU, Kim YJ, Shin DH, Weon HY, Kwon SW, Seong CN, Ka JO	J Microbiol	10.1007/s12275-013-2231-9	2013	*
Phylogeny	Pedobacter boryungensis sp. nov., isolated from soil.	Jung YT, Lee SY, Choi WC, Oh TK, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.028183-0	2011	*
Phylogeny	Pedobacter xixiisoli sp. nov., isolated from bank soil.	Zeng Y, Feng H, Huang Y	Int J Syst Evol Microbiol	10.1099/ijs.0.065946-0	2014	*
Phylogeny	Pedobacter koreensis sp. nov., isolated from fresh water.	Baik KS, Park YD, Kim MS, Park SC, Moon EY, Rhee MS, Choi JH, Seong CN	Int J Syst Evol Microbiol	10.1099/ijs.0.65186-0	2007	*

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 )

#32247

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 #28488 (see below)

#37818 ; Curators of the CIP;

#68371

Automatically annotated from API 50CH acid .

#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 .

#91865

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-ID309552.1 )

#120482 Collection of Institut Pasteur ; Curators of the CIP; CIP 109707

#124043

Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

#28488

IJSEM 2079 2007 ( DOI 10.1099/ijs.0.65186-0 , PubMed 17766875 )

* These data were automatically processed and therefore are not curated

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