Name: Pedobacter ginsengiterrae KCTC 23317
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133768

Type strain:

Species: Pedobacter ginsengiterrae

Culture col. no.: KCTC 23317, JCM 17338, DCY 49

Strain history: D.-C. Yang DCY49.

NCBI tax ID(s): 871696 (species)

Section

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

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

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Sphingobacteriia*
	Order	*Sphingobacteriales*
	Family	*Sphingobacteriaceae*
	Genus	*Pedobacter*
	Species	**Pedobacter ginsengiterrae**
	Full Scientific Name (LPSN)	Pedobacter ginsengiterrae Hoang et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30449]	Gram stain	negative

[Ref.: #30449]	Cell length	2 µm

[Ref.: #30449]	Cell width	0.7 µm

[Ref.: #30449]	Cell shape	rod-shaped

[Ref.: #30449]	Motility	yes

[Ref.: #30449]	Flagellum arrangement	gliding

[Ref.: #30449]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #30449]	growth	04-34 °C
[Ref.: #30449]	optimum	28 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #30449]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30449]			optimum	7
[Ref.: #30449]			growth	4.5-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30449]

Oxygen tolerance

aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30449]		NaCl		growth	0-3	%
[Ref.: #30449]		NaCl		optimum	0.5	%

[Ref.: #30449]	Observation	aggregates in clumps
[Ref.: #67770]	Observation	quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30449]	arabinose ChEBI	+	carbon source
[Ref.: #30449]	cellobiose ChEBI	+	carbon source
[Ref.: #30449]	esculin ChEBI	+	hydrolysis
[Ref.: #30449]	galactose ChEBI	+	carbon source
[Ref.: #30449]	glucose ChEBI	+	carbon source
[Ref.: #30449]	glycogen ChEBI	+	carbon source
[Ref.: #30449]	lactose ChEBI	+	carbon source
[Ref.: #30449]	maltose ChEBI	+	carbon source
[Ref.: #30449]	mannose ChEBI	+	carbon source
[Ref.: #30449]	melibiose ChEBI	+	carbon source
[Ref.: #30449]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #30449]	raffinose ChEBI	+	carbon source
[Ref.: #30449]	rhamnose ChEBI	+	carbon source
[Ref.: #30449]	salicin ChEBI	+	carbon source
[Ref.: #30449]	sucrose ChEBI	+	carbon source
[Ref.: #30449]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #30449]	acid phosphatase	+	3.1.3.2
[Ref.: #30449]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30449]	catalase	+	1.11.1.6
[Ref.: #30449]	cytochrome oxidase	+	1.9.3.1

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

[Ref.: #30449]	Sample type/isolated from	soil

[Ref.: #67770]	Sample type/isolated from	Soil of a ginseng field in a mountainous region of Chungbuk Province
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #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

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.: #30449]	Pedobacter ginsengiterrae strain DCY49 16S ribosomal RNA gene, partial sequence	HM776704	1410	GenBank	871696 tax ID

[Ref.: #30449]	GC-content	40.5 mol%
[Ref.: #67770]	GC-content	40.5 mol%	high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #30449]

Culture collection no.

KCTC 23317, JCM 17338, DCY 49

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 )

#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 (see below)

#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 .

#26784

IJSEM 1273 2013 ( DOI 10.1099/ijs.0.036376-0 , PubMed 22771687 )

* These data were automatically processed and therefore are not curated

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