Pedobacter daechungensis (KCTC 12637, LMG 23489, Dae 13)

Name: Pedobacter daechungensis (KCTC 12637, LMG 23489, Dae 13)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133430

Type strain

Culture col. no. KCTC 12637 LMG 23489 Dae 13

NCBI tax ID(s) 398054

Special Collections KCTC Literature strains

History KCTC <- ST Lee, KAIST

Links

Pedobacter daechungensis KCTC 12637 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from freshwater .

Gram-negative rod-shaped aerobe 16S sequence Bacteria

Name and taxonomic classification

SI-ID 290310

LMG 23489,KCTC 12637

@ref 20215

Last LPSN update 2026-05-29 08:38:05

Domain Bacteria

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Pedobacter

Species Pedobacter daechungensis

Full scientific name Pedobacter daechungensis An et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
28918	negative	1.05 µm	0.35 µm	rod-shaped
67771				rod-shaped
67771	negative

Pigmentation

28918

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
28918	positive	growth	15-30
28918	positive	optimum	30
67771	positive	growth	30

Culture pH

@ref	Ability	Type	PH
28918	positive	optimum	7
28918	positive	growth	05-08

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
28918	aerobe
67771	aerobe

Spore formation

28918

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
28918	NaCl	positive	growth	<1 %

Observation

67771

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
28918	22599 ChEBI	arabinose	+	carbon source
28918	16947 ChEBI	citrate	+	carbon source
28918	4853 ChEBI	esculin	+	hydrolysis
28918	24265 ChEBI	gluconate	+	carbon source
28918	17234 ChEBI	glucose	+	carbon source
28918	24996 ChEBI	lactate	+	carbon source
28918	17306 ChEBI	maltose	+	carbon source
28918	29864 ChEBI	mannitol	+	carbon source
28918	37684 ChEBI	mannose	+	carbon source
28918	506227 ChEBI	N-acetylglucosamine	+	carbon source
28918	26546 ChEBI	rhamnose	+	carbon source
28918	17822 ChEBI	serine	+	carbon source
28918	17992 ChEBI	sucrose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
28918	alkaline phosphatase	+	3.1.3.1
28918	catalase	+	1.11.1.6
28918	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Pond (small)
#Environmental	#Aquatic	#River (Creek)

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
28918	freshwater (river, lake, pond)
67771	From sediment, freshwater lake in Daejeon	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB267722 (>99% sequence identity) for Pedobacter daechungensis subclade from Microbeatlas

Aquatic Samples	195
Soil Samples	32
Animal Samples	77
Plant Samples	1
Total Samples	305

Interaction and safety

Sequence information

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
28918	Pedobacter daechungensis gene for 16S rRNA, partial sequence, strain: Dae 13	AB267722	1467		398054

GC content

28918

GC-content (mol%)33.8

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
	Aurantibacillus circumpalustris gen. nov., sp. nov., the first characterized representative of the Bacteroidota candidate family env.OPS 17 and proposal of Aurantibacillaceae fam. nov.	Vieira S, Riedel T, Geppert A, Rohde M, Wolf J, Neumann-Schaal M, Overmann J.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006134	2023
	Pedobacter alpinus sp. nov., isolated from a plateau lake.	Li AH, Liu HC, Zhou YG.	Int J Syst Evol Microbiol	10.1099/ijsem.0.000498	2015
Phylogeny	Pedobacter pituitosus sp. nov., isolated from a waterfall.	Chun J, Kang JY, Jahng KY.	Int J Syst Evol Microbiol	10.1099/ijs.0.065235-0	2014
Phylogeny	Pedobacter silvilitoris sp. nov., isolated from wood falls.	Park S, Jung YT, Park JM, Won SM, Yoon JH.	Int J Syst Evol Microbiol	10.1099/ijs.0.000098	2015
Phylogeny	Pedobacter soyangensis sp. nov., isolated from Lake Soyang in Korea.	Joung Y, Kang H, Kim H, Lee BI, Kwon OS, Joh K.	J Microbiol	10.1007/s12275-014-3284-0	2014
Phylogeny	Pedobacter rivuli sp. nov., isolated from a freshwater stream.	Kang H, Kim H, Joung Y, Joh K	Int J Syst Evol Microbiol	10.1099/ijs.0.067579-0	2014
Phylogeny	Pedobacter arcticus sp. nov., a facultative psychrophile isolated from Arctic soil, and emended descriptions of the genus Pedobacter, Pedobacter heparinus, Pedobacter daechungensis, Pedobacter terricola, Pedobacter glucosidilyticus and Pedobacter lentus.	Zhou Z, Jiang F, Wang S, Peng F, Dai J, Li W, Fang C	Int J Syst Evol Microbiol	10.1099/ijs.0.031104-0	2011
Phylogeny	Pedobacter aquicola sp. nov., isolated from freshwater.	Joung Y, Jang HJ, Park M, Song J, Cho JC	J Microbiol	10.1007/s12275-018-7499-3	2018
Phylogeny	Pedobacter daechungensis sp. nov., from freshwater lake sediment in South Korea.	An DS, Kim SG, Ten LN, Cho CH	Int J Syst Evol Microbiol	10.1099/ijs.0.001529-0	2009

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 )
#25357	IJSEM 69 2009 ( DOI 10.1099/ijs.0.001529-0 , PubMed 19126726 )
#28918	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 #25357
#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 .
#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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Pedobacter daechungensis (KCTC 12637, LMG 23489, Dae 13)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

BacDive

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