Pedobacter kyonggii (KEMB 9005-574, KACC 19174, JCM 31916)

Name: Pedobacter kyonggii (KEMB 9005-574, KACC 19174, JCM 31916)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 141159

Type strain

Strain Designation K-4-11-1

Culture col. no. KEMB 9005-574 KACC 19174 JCM 31916 K-4-11-1

NCBI tax ID(s) 1926871

Special Collections JCM Literature strains

History J. Kim; Kyonggi Univ., South Korea; K-4-11-1.

Links

Pedobacter kyonggii K-4-11-1 is an obligate aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from forest soil.

Gram-negative rod-shaped colony-forming obligate aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 393327

JCM 31916

@ref 20215

Last LPSN update 2026-02-09 11:33:50

Domain Bacteria

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Pedobacter

Species Pedobacter kyonggii

Full scientific name Pedobacter kyonggii Chaudhary et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
44080	negative	1.3-1.7 µm	0.8-1.0 µm	rod-shaped
125439	negative					99.7

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
44080	1.5-2.5 mm	light salmon	circular	5 days	R2A agar

Culture and growth conditions

Culture medium

@ref	Name	Growth
44080	BHI
44080	LBA
44080	Nutrient agar (NA)
44080	Reasoner's 2A agar (R2A)
44080	Trypticase Soy Agar (TSA)
44080	MacConkey
44080	Marine agar (MA)

Culture temp

@ref	Growth	Type	Temperature (°C)
44080	positive	growth	0-32
44080	positive	optimum	10-28
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
44080	positive	optimum	6.5-8.5
44080	positive	growth	5.0-10.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
44080	obligate aerobe
125439	obligate aerobe	97.4

Spore formation

@ref	Spore formation	Confidence
44080
125439		98.7

Halophily

@ref	Halophily level	Salt	Growth	Tested relation	Concentration
44080		NaCl	positive	growth	0-1.5 %(w/v)
44080	non-halophilic	NaCl	positive	optimum	0 %(w/v)

Observation

67770

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
44080	16193 ChEBI	3-hydroxybenzoate	-	assimilation
44080	37054 ChEBI	3-hydroxybutyrate	-	assimilation
44080	17879 ChEBI	4-hydroxybenzoate	-	assimilation
44080	355715 ChEBI	4-nitrophenyl beta-D-galactopyranoside	+	assimilation
44080	17128 ChEBI	adipate	-	assimilation
44080	85146 ChEBI	carboxymethylcellulose	+	hydrolysis
44080		casein	+	hydrolysis
44080	17029 ChEBI	chitin	-	hydrolysis
44080	17634 ChEBI	D-glucose	+	assimilation
44080	16899 ChEBI	D-mannitol	-	assimilation
44080	16024 ChEBI	D-mannose	+	assimilation
44080	16988 ChEBI	D-ribose	-	assimilation
44080	17924 ChEBI	D-sorbitol	-	assimilation
44080	27689 ChEBI	decanoate	-	assimilation
44080	16991 ChEBI	dna	-	hydrolysis
44080	4853 ChEBI	esculin	+	hydrolysis
44080		esculin ferric citrate	+	assimilation
44080	5291 ChEBI	gelatin	+	assimilation
44080	5291 ChEBI	gelatin	+	hydrolysis
44080	17234 ChEBI	glucose	-	fermentation
44080	28087 ChEBI	glycogen	-	assimilation
44080	17240 ChEBI	itaconate	-	assimilation
44080	16977 ChEBI	L-alanine	-	assimilation
44080	30849 ChEBI	L-arabinose	+	assimilation
44080	16467 ChEBI	L-arginine	-	assimilation
44080	18287 ChEBI	L-fucose	-	assimilation
44080	15971 ChEBI	L-histidine	-	assimilation
44080	17203 ChEBI	L-proline	+	assimilation
44080	62345 ChEBI	L-rhamnose	+	assimilation
44080	17115 ChEBI	L-serine	-	assimilation
44080	16828 ChEBI	L-tryptophan	-	assimilation
44080	24996 ChEBI	lactate	-	assimilation
44080	25115 ChEBI	malate	-	assimilation
44080	17306 ChEBI	maltose	+	assimilation
44080	28053 ChEBI	melibiose	+	assimilation
44080	17268 ChEBI	myo-inositol	-	assimilation
44080	506227 ChEBI	N-acetylglucosamine	+	assimilation
44080	17632 ChEBI	nitrate	-	reduction
44080	18401 ChEBI	phenylacetate	-	assimilation
44080		potassium 2-dehydro-D-gluconate	-	assimilation
44080		potassium 5-dehydro-D-gluconate	-	assimilation
44080	32032 ChEBI	potassium gluconate	-	assimilation
44080	17272 ChEBI	propionate	-	assimilation
44080	17814 ChEBI	salicin	+	assimilation
44080	32954 ChEBI	sodium acetate	-	assimilation
44080	53258 ChEBI	sodium citrate	-	assimilation
44080	62983 ChEBI	sodium malonate	-	assimilation
44080	28017 ChEBI	starch	-	hydrolysis
44080	9300 ChEBI	suberic acid	-	assimilation
44080	17992 ChEBI	sucrose	+	assimilation
44080	53423 ChEBI	tween 40	+	hydrolysis
44080	53426 ChEBI	tween 80	+/-	hydrolysis
44080	18186 ChEBI	tyrosine	-	hydrolysis
44080	16199 ChEBI	urea	-	assimilation
44080	31011 ChEBI	valerate	-	assimilation

Metabolite production

@ref	Chebi-ID	Metabolite
44080	15688 ChEBI	acetoin
44080	16136 ChEBI	hydrogen sulfide
44080	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
44080	15688 ChEBI	acetoin	-
44080	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
44080	acid phosphatase	+	3.1.3.2
44080	alkaline phosphatase	+	3.1.3.1
44080	alpha-chymotrypsin	+	3.4.21.1
44080	alpha-fucosidase	+/-	3.2.1.51
44080	alpha-galactosidase	+	3.2.1.22
44080	alpha-glucosidase	+	3.2.1.20
44080	alpha-mannosidase	+	3.2.1.24
44080	beta-galactosidase	-	3.2.1.23
44080	beta-glucosidase	+	3.2.1.21
44080	beta-glucuronidase	-	3.2.1.31
44080	catalase	+	1.11.1.6
44080	cystine arylamidase	+	3.4.11.3
44080	cytochrome oxidase	+	1.9.3.1
44080	esterase (C 4)	+/-
44080	esterase Lipase (C 8)	+/-
44080	leucine arylamidase	+	3.4.11.1
44080	lipase (C 14)	-
44080	N-acetyl-beta-glucosaminidase	+	3.2.1.52
44080	naphthol-AS-BI-phosphohydrolase	-
44080	trypsin	+	3.4.21.4
44080	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

44080

Fatty acid	Percentage
C16:1ω7c / C16:1ω6c	29.3
C15:0 iso	27
C17:0 iso 3OH	12.8
C17:0 anteiso	8.3
C17:1 iso ω9c / C16:0 10-methyl	4.7
C15:0 iso 3OH	2.6
C16:0	2.2
C17:1 I / anteiso C17:1 B	1.5
C16:1ω5c	1.4
C16:0 3OH	1.4
C14:0	1.2
C15:1ω6c	1.1
C16:0 iso 3OH	0.9
C15:0 anteiso	0.9
C18:1ω5c	0.6
C18:0	0.5
C16:1 iso H	0.5
C17:0 2OH	0.5
C15:1 iso F	0.4
C17:0 iso	0.4
C14:0 2OH	0.4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
44080	forest soil	Kyonggi University, Suwon	Republic of Korea	KOR	Asia
67770	Forest soil of Kyonggi University	Suwon	Republic of Korea	KOR	Asia

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM431066v1 assembly for Pedobacter kyonggii K-4-11-1	contig	GCA_004310665	1926871.3	2882023792	1926871	62.96

16S sequences

@ref	Description	Accession	Database
44080	Pedobacter kyonggii strain K-4-11-1 16S ribosomal RNA gene, partial sequence	KY313409

GC content

@ref	GC-content (mol%)	Method
67770	38.3	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pedobacter kyonggii K-4-11-1
NCBI: GCA_004310665

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.70	no
125439	motility	BacteriaNetⓘ	no	74.00	no
125439	gram_stain	BacteriaNetⓘ	negative	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.40	no

Literature

Topic	Title	Authors	Journal	DOI	Year
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

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 )
#44080	Dhiraj Kumar Chaudhary, Sang Don Lee and Jaisoo Kim: Pedobacter kyonggii sp. nov., a psychrotolerant bacterium isolated from forest soil. IJSEM 67: 5120 - 5127 2017 ( DOI 10.1099/ijsem.0.002428 , PubMed 29047421 )
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#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 )

Rate our new design

Content

About us

Pedobacter kyonggii (KEMB 9005-574, KACC 19174, JCM 31916)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_004310665

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media