Pedobacter ginsengiterrae (KCTC 23317, JCM 17338, DCY 49)

Name: Pedobacter ginsengiterrae (KCTC 23317, JCM 17338, DCY 49)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133768

Type strain

Culture col. no. KCTC 23317 JCM 17338 DCY 49

NCBI tax ID(s) 871696

Special Collections JCM KCTC Literature strains

History D.-C. Yang DCY49.

Links

Pedobacter ginsengiterrae KCTC 23317 is an aerobe, Gram-negative, motile bacterium that was isolated from soil.

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

Name and taxonomic classification

SI-ID 286488

KCTC 23317,JCM 17338

@ref 20215

Last LPSN update 2026-02-09 11:32:01

Domain Bacteria

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Pedobacter

Species Pedobacter ginsengiterrae

Full scientific name Pedobacter ginsengiterrae Hoang et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Flagellum arrangement
30449	negative	2 µm	0.7 µm	rod-shaped		gliding

Pigmentation

30449

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
30449	positive	growth	04-34
30449	positive	optimum	28
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
30449	positive	optimum	7
30449	positive	growth	4.5-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

30449

Oxygen toleranceaerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30449	NaCl	positive	growth	0-3 %
30449	NaCl	positive	optimum	0.5 %

Observation

@ref	Observation
30449	aggregates in clumps
67770	quinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30449	22599 ChEBI	arabinose	+	carbon source
30449	17057 ChEBI	cellobiose	+	carbon source
30449	4853 ChEBI	esculin	+	hydrolysis
30449	28260 ChEBI	galactose	+	carbon source
30449	17234 ChEBI	glucose	+	carbon source
30449	28087 ChEBI	glycogen	+	carbon source
30449	17716 ChEBI	lactose	+	carbon source
30449	17306 ChEBI	maltose	+	carbon source
30449	37684 ChEBI	mannose	+	carbon source
30449	28053 ChEBI	melibiose	+	carbon source
30449	506227 ChEBI	N-acetylglucosamine	+	carbon source
30449	16634 ChEBI	raffinose	+	carbon source
30449	26546 ChEBI	rhamnose	+	carbon source
30449	17814 ChEBI	salicin	+	carbon source
30449	17992 ChEBI	sucrose	+	carbon source
30449	27082 ChEBI	trehalose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30449	acid phosphatase	+	3.1.3.2
30449	alkaline phosphatase	+	3.1.3.1
30449	catalase	+	1.11.1.6
30449	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
30449	soil
67770	Soil of a ginseng field in a mountainous region of Chungbuk Province	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence HM776704 (>99% sequence identity) for Pedobacter from Microbeatlas

Aquatic Samples	1652
Soil Samples	2160
Animal Samples	1898
Plant Samples	1902
Total Samples	7612

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3953738v1 assembly for Pedobacter ginsengiterrae JCM 17338	scaffold	GCA_039537385	871696	68.18

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
30449	Pedobacter ginsengiterrae strain DCY49 16S ribosomal RNA gene, partial sequence	HM776704	1410		871696

GC content

@ref	GC-content (mol%)	Method
30449	40.5
67770	40.5	high performance liquid chromatography (HPLC)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pedobacter jejuensis sp. nov., isolated from soil of a pine grove, and emended description of the genus Pedobacter.	Kook M, Park Y, Yi TH	Int J Syst Evol Microbiol	10.1099/ijs.0.058024-0	2014
Phylogeny	Pedobacter ginsengiterrae sp. nov., isolated from soil of a ginseng field.	Hoang VA, Kim YJ, Nguyen NL, Min JW, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.036376-0	2012
Phylogeny	Pedobacter mucosus sp. nov., isolated from a soil sample of glacier foreland in Austre Lovenbreen, Arctic.	Huang J, Peng X, Qin K, Liu Y, Niu J, Liu J, Dong J, Zhang Y, Peng F	Int J Syst Evol Microbiol	10.1099/ijsem.0.005448	2022

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 )
#26784	IJSEM 1273 2013 ( DOI 10.1099/ijs.0.036376-0 , PubMed 22771687 )
#30449	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 #26784
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Pedobacter ginsengiterrae (KCTC 23317, JCM 17338, DCY 49)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_039537385

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

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