Name: Pedobacter suwonensis 15-52
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 14101

Type strain:

Species: Pedobacter suwonensis

Strain Designation: 15-52

Culture col. no.: DSM 18130, CIP 109582, KACC 11317

Strain history: CIP <- 2007, DSMZ <- KACC <- H.Y. Weon, RDA, Suwon, Korea: strain 15-52

NCBI tax ID(s): 332999 (species)

SI-ID 297288

DSM 18130, KACC 11317, CIP 109582

Special Collections

Section

When using BacDive for research please cite our paper

Pedobacter suwonensis 15-52 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from rhizosphere soil of Chinese cabbage .

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

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 suwonensis**
	Full Scientific Name (LPSN)	Pedobacter suwonensis Kwon et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #31756]	Gram stain	negative
[Ref.: #123391]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %96.944
[Ref.: #125439]	Gram stain	negative Confidence in %99.8

[Ref.: #31756]	Cell length	2.3 µm

[Ref.: #31756]	Cell width	0.65 µm

[Ref.: #31756]	Cell shape	rod-shaped
[Ref.: #123391]	Cell shape	rod-shaped

[Ref.: #31756]	Motility	no
[Ref.: #123391]	Motility	no

[Ref.: #31756]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7400]

Culture medium

TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)

[Ref.: #7400]

Culture medium growth

[Ref.: #7400]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7400]

Culture medium composition

expand / minimize

[Ref.: #37773]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #37773]

Culture medium growth

[Ref.: #37773]

Culture medium composition

expand / minimize

[Ref.: #123391]

Culture medium

CIP Medium 72

[Ref.: #123391]

Culture medium growth

[Ref.: #123391]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #7400]	growth	30 °C
[Ref.: #31756]	growth	01-37 °C
[Ref.: #31756]	optimum	34 °C
[Ref.: #37773]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #31756]			optimum	6.75
[Ref.: #31756]			growth	5.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31756]	Oxygen tolerance	aerobe
[Ref.: #123391]	Oxygen tolerance	obligate aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %95.4

[Ref.: #31756]	Ability of spore formation	no
[Ref.: #125439]	Ability of spore formation	no Confidence in %98.1

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31756]		NaCl		growth	0-3	%
[Ref.: #31756]		NaCl		optimum	0.25	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31756]	arabinose ChEBI	+	carbon source
[Ref.: #31756]	cellobiose ChEBI	+	carbon source
[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-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.: #31756]	esculin ChEBI	+	hydrolysis
[Ref.: #31756]	fructose ChEBI	+	carbon source
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31756]	galactose ChEBI	+	carbon source
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31756]	glucose ChEBI	+	carbon source
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31756]	glycogen ChEBI	+	carbon source
[Ref.: #68371]	glycogen ChEBI	-	builds acid from	* from API 50CH acid
[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-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.: #31756]	lactose ChEBI	+	carbon source
[Ref.: #31756]	maltose ChEBI	+	carbon source
[Ref.: #31756]	mannose ChEBI	+	carbon source
[Ref.: #31756]	melibiose ChEBI	+	carbon source
[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.: #31756]	methyl D-glucoside ChEBI	+	carbon source
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31756]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #123391]	nitrate ChEBI	-	reduction
[Ref.: #123391]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31756]	raffinose ChEBI	+	carbon source
[Ref.: #31756]	rhamnose ChEBI	+	carbon source
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31756]	salicin ChEBI	+	carbon source
[Ref.: #31756]	sucrose ChEBI	+	carbon source
[Ref.: #31756]	trehalose ChEBI	+	carbon source
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31756]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #123391]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #31756]	acid phosphatase	+	3.1.3.2
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #31756]	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.: #31756]	catalase	+	1.11.1.6
[Ref.: #123391]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #31756]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #31756]	gelatinase	+
[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.: #123391]	oxidase	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #123391]	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.: #123391]	11605	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.: #123391]	11975	-	+	+	+	-	+	+	+	+	-	+	+	+	+	-	+	+	+	+	+

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

[Ref.: #7400]	Sample type/isolated from	rhizosphere soil of Chinese cabbage (Brassica campestris)
[Ref.: #7400]	Host species	Brassica campestris
[Ref.: #7400]	Country	Republic of Korea
[Ref.: #7400]	Country ISO 3 Code	KOR
[Ref.: #7400]	Continent	Asia

[Ref.: #123391]	Sample type/isolated from	Environment, Rhizosphere soil, Chinese cabbage Brassica campestris
[Ref.: #123391]	Geographic location (country and/or sea, region)	Suwon
[Ref.: #123391]	Country	Republic of Korea
[Ref.: #123391]	Country ISO 3 Code	KOR
[Ref.: #123391]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ097274 (>99% sequence identity) for Pedobacter from Microbeatlas

Aquatic Samples	64
Soil Samples	113
Animal Samples	279
Plant Samples	109
Total Samples	565

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

[Ref.: #7400]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #123391]	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.: #7400]	Pedobacter suwonensis strain 15-52 16S ribosomal RNA gene, partial sequence	DQ097274	1444	GenBank ENA	332999 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pedobacter suwonensis DSM 18130	GCA_900111825	scaffold	GenBank ENA	332999 tax ID	*
[Ref.: #66792]	Pedobacter suwonensis strain DSM 18130	332999.8	wgs	PATRIC	332999 tax ID	*
[Ref.: #66792]	Pedobacter suwonensis DSM 18130	2622736524	draft	JGI IMG/M	332999 tax ID	*

[Ref.: #7400]

GC-content

44.2 mol%

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pedobacter suwonensis DSM 18130 NCBI: GCA_900111825.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	96.944	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.884	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	79.11	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	85.11	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	95.99	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	85.5	yes

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pedobacter suwonensis DSM 18130 NCBI: GCA_900111825
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	98.1
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	72.1
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.8
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	95.4

Availability in culture collections External links

[Ref.: #7400]

Culture collection no.

DSM 18130, CIP 109582, KACC 11317

[Ref.: #83269]

SI-ID 297288

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pedobacter riviphilus sp. nov., isolated from stream sediment.	Im HS, Joung Y, Lee SS	Int J Syst Evol Microbiol	10.1099/ijsem.0.004989	2021	*
Phylogeny	Pedobacter kyonggii sp. nov., a psychrotolerant bacterium isolated from forest soil.	Chaudhary DK, Lee SD, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002428	2017	*
Phylogeny	Pedobacter zeae sp. nov., an endophytic bacterium isolated from maize root.	Gao JL, Sun P, Mao XJ, Du YL, Liu BY, Sun JG	Int J Syst Evol Microbiol	10.1099/ijsem.0.001603	2017	*
Phylogeny	Pedobacter vanadiisoli sp. nov., isolated from soil of a vanadium mine.	Wang Z, Tan Y, Xu D, Wang G, Yuan J, Zheng S	Int J Syst Evol Microbiol	10.1099/ijsem.0.001480	2016	*
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 rhizosphaerae sp. nov. and Pedobacter soli sp. nov., isolated from rhizosphere soil of Chinese cabbage (Brassica campestris).	Kwon SW, Son JA, Kim SJ, Kim YS, Park IC, Bok JI, Weon HY	Int J Syst Evol Microbiol	10.1099/ijs.0.026781-0	2011	*
Phylogeny	Pedobacter agri sp. nov., from soil.	Roh SW, Quan ZX, Nam YD, Chang HW, Kim KH, Kim MK, Im WT, Jin L, Kim SH, Lee ST, Bae JW	Int J Syst Evol Microbiol	10.1099/ijs.0.65783-0	2008	*
Phylogeny	Pedobacter suwonensis sp. nov., isolated from the rhizosphere of Chinese cabbage (Brassica campestris).	Kwon SW, Kim BY, Lee KH, Jang KY, Seok SJ, Kwon JS, Kim WG, Weon HY	Int J Syst Evol Microbiol	10.1099/ijs.0.64196-0	2007	*

References

#7400

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18130

#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 )

#31756

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 #28029 (see below)

#37773 ; Curators of the CIP;

#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) .

#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 .

#83269

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-ID297288.1 )

#123391 Collection of Institut Pasteur ; Curators of the CIP; CIP 109582

#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 .

#28029

IJSEM 480 2007 ( DOI 10.1099/ijs.0.64196-0 , PubMed 17329772 )

* These data were automatically processed and therefore are not curated

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Pedobacter suwonensis DSM 18130

Pedobacter suwonensis DSM 18130

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