Name: Pedobacter daechungensis KCTC 12637
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133430

Type strain:

Species: Pedobacter daechungensis

Culture col. no.: KCTC 12637, LMG 23489, Dae 13

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 398054 (species)

SI-ID 290310

LMG 23489, KCTC 12637

Section

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

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 daechungensis**
	Full Scientific Name (LPSN)	Pedobacter daechungensis An et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #28918]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative

[Ref.: #28918]	Cell length	1.05 µm

[Ref.: #28918]	Cell width	0.35 µm

[Ref.: #28918]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #28918]	Motility	no
[Ref.: #67771]	Motility	no

[Ref.: #28918]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #28918]	growth	15-30 °C
[Ref.: #28918]	optimum	30 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #28918]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #28918]			optimum	7
[Ref.: #28918]			growth	05-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #28918]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #28918]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #28918]		NaCl		growth	<1	%

[Ref.: #67771]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #28918]	arabinose ChEBI	+	carbon source
[Ref.: #28918]	citrate ChEBI	+	carbon source
[Ref.: #28918]	esculin ChEBI	+	hydrolysis
[Ref.: #28918]	gluconate ChEBI	+	carbon source
[Ref.: #28918]	glucose ChEBI	+	carbon source
[Ref.: #28918]	lactate ChEBI	+	carbon source
[Ref.: #28918]	maltose ChEBI	+	carbon source
[Ref.: #28918]	mannitol ChEBI	+	carbon source
[Ref.: #28918]	mannose ChEBI	+	carbon source
[Ref.: #28918]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #28918]	rhamnose ChEBI	+	carbon source
[Ref.: #28918]	serine ChEBI	+	carbon source
[Ref.: #28918]	sucrose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #28918]	alkaline phosphatase	+	3.1.3.1
[Ref.: #28918]	catalase	+	1.11.1.6
[Ref.: #28918]	cytochrome oxidase	+	1.9.3.1

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

[Ref.: #28918]	Sample type/isolated from	freshwater (river, lake, pond)

[Ref.: #67771]	Sample type/isolated from	From sediment, freshwater lake in Daejeon
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

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.: #28918]	Pedobacter daechungensis gene for 16S rRNA, partial sequence, strain: Dae 13	AB267722	1467	GenBank	398054 tax ID

[Ref.: #28918]

GC-content

33.8 mol%

Availability in culture collections External links

[Ref.: #28918]

Culture collection no.

KCTC 12637, LMG 23489, Dae 13

[Ref.: #91435]

SI-ID 290310

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 )

#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 (see below)

#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 .

#91435

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-ID290310.1 )

#25357

IJSEM 69 2009 ( DOI 10.1099/ijs.0.001529-0 , PubMed 19126726 )

* These data were automatically processed and therefore are not curated

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