Pedobacter humicola (KEMB 9005-332, KACC 18452, JCM 31010)

Name: Pedobacter humicola (KEMB 9005-332, KACC 18452, JCM 31010)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 163933

Type strain

Culture col. no. KEMB 9005-332 KACC 18452 JCM 31010

NCBI tax ID(s) 1752078

Special Collections JCM

History JCM <-- J. Kim; Kyonggi Univ., South Korea; R135.

Links

Pedobacter humicola JCM 31010 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from soil in Hwaseong, South Korea.

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

Name and taxonomic classification

SI-ID 133718

JCM 31010

@ref 20215

Last LPSN update 2026-05-29 08:45:17

Domain Bacteria

Phylum Bacteroidota

Class Sphingobacteriia

Order Sphingobacteriales

Family Sphingobacteriaceae

Genus Pedobacter

Species Pedobacter humicola

Full scientific name Pedobacter humicola Dahal and Kim 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
43974	negative	1.0-1.4 µm	0.6-0.9 µm	rod-shaped

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43974	1.0-2.0 mm	light pink	circular	4 days	R2A agar

Pigmentation

@ref	Production	Name
43974		flexirubin type pigments

Culture and growth conditions

Culture medium

@ref	Name	Growth
43974	LB (Luria-Bertani) MEDIUM
43974	Marine agar (MA)
43974	Nutrient agar (NA)
43974	Reasoner's 2A agar (R2A)
43974	Tryptone soya agar
43974	MacConkey agar

Culture temp

@ref	Growth	Type	Temperature (°C)
43974	positive	growth	10-42
43974	positive	optimum	25-32
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
43974	positive	optimum	6.5-8.5
43974	positive	growth	5.0-10.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

43974

Oxygen toleranceaerobe

Spore formation

43974

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43974	NaCl	positive	optimum	0 %(w/v)
43974	NaCl	positive	growth	0-6 %(w/v)

Observation

67770

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43974	16808 ChEBI	2-dehydro-D-gluconate	-	builds acid from
43974	16193 ChEBI	3-hydroxybenzoate	+/-	builds acid from
43974	37054 ChEBI	3-hydroxybutyrate	-	builds acid from
43974	17879 ChEBI	4-hydroxybenzoate	+/-	builds acid from
43974	355715 ChEBI	4-nitrophenyl beta-D-galactopyranoside	+	builds acid from
43974	58143 ChEBI	5-dehydro-D-gluconate	-	builds acid from
43974	17128 ChEBI	adipate	+/-	builds acid from
43974		casein	-	assimilation
43974	17634 ChEBI	D-glucose	-	builds acid from
43974	17634 ChEBI	D-glucose	+	builds acid from
43974	16899 ChEBI	D-mannitol	-	builds acid from
43974	16988 ChEBI	D-ribose	-	builds acid from
43974	33801 ChEBI	D-saccharate	+	builds acid from
43974	17924 ChEBI	D-sorbitol	-	builds acid from
43974	27689 ChEBI	decanoate	-	builds acid from
43974		esculin ferric citrate	+	builds acid from
43974	5291 ChEBI	gelatin	+	builds acid from
43974	17234 ChEBI	glucose	-	fermentation
43974	17234 ChEBI	glucose	+	assimilation
43974	28087 ChEBI	glycogen	-	builds acid from
43974	17240 ChEBI	itaconate	-	builds acid from
43974	16977 ChEBI	L-alanine	-	builds acid from
43974	30849 ChEBI	L-arabinose	+	builds acid from
43974	16467 ChEBI	L-arginine	-	builds acid from
43974	18287 ChEBI	L-fucose	-	builds acid from
43974	15971 ChEBI	L-histidine	-	builds acid from
43974	17203 ChEBI	L-proline	-	builds acid from
43974	62345 ChEBI	L-rhamnose	+	builds acid from
43974	17115 ChEBI	L-serine	-	builds acid from
43974	16828 ChEBI	L-tryptophan	-	builds acid from
43974	24996 ChEBI	lactate	+/-	builds acid from
43974	25115 ChEBI	malate	+	builds acid from
43974	17306 ChEBI	maltose	+	builds acid from
43974	37684 ChEBI	mannose	+	builds acid from
43974	28053 ChEBI	melibiose	+	builds acid from
43974	17268 ChEBI	myo-inositol	-	builds acid from
43974	506227 ChEBI	N-acetylglucosamine	+	builds acid from
43974	17632 ChEBI	nitrate	+	reduction
43974	18401 ChEBI	phenylacetate	-	builds acid from
43974	32032 ChEBI	potassium gluconate	+/-	builds acid from
43974	17272 ChEBI	propionate	+	builds acid from
43974	17814 ChEBI	salicin	+	builds acid from
43974	32954 ChEBI	sodium acetate	+	builds acid from
43974	53258 ChEBI	sodium citrate	-	builds acid from
43974	62983 ChEBI	sodium malonate	-	builds acid from
43974	28017 ChEBI	starch	-	assimilation
43974	9300 ChEBI	suberic acid	-	builds acid from
43974	53426 ChEBI	tween 80	+	hydrolysis
43974	16199 ChEBI	urea	-	builds acid from
43974	31011 ChEBI	valerate	+	builds acid from

Antibiotic resistance

@ref	ChEBI	Metabolite	Sensitivity conc.	Resistance conc.
43974	28971	ampicillin
43974	17698	chloramphenicol	100 µg (disc)
43974	27641	cycloheximide
43974	17833	gentamicin	10 µg (disc)
43974	6104	kanamycin	30 µg (disc)
43974	100147	nalidixic acid		30 µg (disc)
43974	7507	neomycin	30 µg (disc)
43974	28368	novobiocin		30 µg (disc)
43974	17334	penicillin
43974	28077	rifampicin	30 µg (disc)
43974	17076	streptomycin
43974	9332	sulfamethoxazole		30 µg (disc)
43974	27902	tetracycline
43974	45924	trimethoprim	30 µg (disc)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43974	16136 ChEBI	hydrogen sulfide

Enzymes

@ref	Value	Activity	Ec
43974	acid phosphatase	+	3.1.3.2
43974	alkaline phosphatase	+	3.1.3.1
43974	alpha-chymotrypsin	+/-	3.4.21.1
43974	alpha-fucosidase	-	3.2.1.51
43974	alpha-galactosidase	+	3.2.1.22
43974	alpha-glucosidase	+	3.2.1.20
43974	alpha-mannosidase	+/-	3.2.1.24
43974	beta-galactosidase	+	3.2.1.23
43974	beta-glucosidase	+	3.2.1.21
43974	beta-glucuronidase	-	3.2.1.31
43974	catalase	+	1.11.1.6
43974	cystine arylamidase	+	3.4.11.3
43974	cytochrome oxidase	-	1.9.3.1
43974	DNase	-
43974	esterase (C 4)	-
43974	esterase Lipase (C 8)	-
43974	leucine arylamidase	+	3.4.11.1
43974	lipase (C 14)	-
43974	N-acetyl-beta-glucosaminidase	+	3.2.1.52
43974	naphthol-AS-BI-phosphohydrolase	+
43974	trypsin	+	3.4.21.4
43974	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

43974

Fatty acid	Percentage
C16:1ω7c / C16:1ω6c	37
C15:0 iso	19.2
C17:0 iso 3OH	8.1
C16:0	6
C16:1ω5c	2.7
C14:0	2.7
C16:0 10-methyl / iso-C17:1ω9c	2.4
10-methyl C18:0	2.2
C18:1ω9c	2.1
C16:0 3OH	2.1
C15:0 iso 3OH	2
C15:0 anteiso	1.9
C16:0 iso 3OH	1.6
C15:1ω6c	1.2
C11:0 anteiso	1.1

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture duration	Enrichment culture temperature
43974	soil in Hwaseong, South Korea	Hwaseong	Republic of Korea	KOR	Asia	37.2694	126.762 37.2694/126.762	R2A agar	2 weeks	28
67770	Soil in Hwaseong	Gyeonggi-do	Republic of Korea	KOR	Asia

Interaction and safety

Sequence information

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Pedobacter humicola strain R135 16S ribosomal RNA gene, partial sequence	KT032156	1449		1752078

GC content

@ref	GC-content (mol%)	Method
67770	40.4	high performance liquid chromatography (HPLC)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pedobacter miscanthi sp. nov., isolated from Miscanthus sinensis.	Chen Z, Tian W, Sun F, Chen Y, Han H, Yao L, Zhang Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.003161	2019
Phylogeny	Pedobacter humicola sp. nov., a member of the genus Pedobacter isolated from soil.	Dahal RH, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.001010	2016

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 )
#43974	Ram Hari Dahal, Jaisoo Kim: Pedobacter humicola sp. nov., a member of the genus Pedobacter isolated from soil. IJSEM 66: 2205 - 2211 2016 ( DOI 10.1099/ijsem.0.001010 , PubMed 26956360 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 )

Content

About us

Pedobacter humicola (KEMB 9005-332, KACC 18452, JCM 31010)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation

Interaction and safety

Sequence information

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

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