Niabella pedocola (KEMB 9005-329, KACC 18454, JCM 31011)

Name: Niabella pedocola (KEMB 9005-329, KACC 18454, JCM 31011)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140823

Type strain

Strain Designation R384

Culture col. no. KEMB 9005-329 KACC 18454 JCM 31011 R384

NCBI tax ID(s) 1752077

Special Collections JCM Literature strains

Links

Niabella pedocola R384 is an aerobe, Gram-negative, rod-shaped prokaryote that forms circular colonies and was isolated from Soil.

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

Name and taxonomic classification

SI-ID 131817

JCM 31011

@ref 20215

Last LPSN update 2025-12-16 10:03:41

Domain Pseudomonadati

Phylum Bacteroidota

Class Chitinophagia

Order Chitinophagales

Family Chitinophagaceae

Genus Niabella

Species Niabella pedocola

Full scientific name Niabella pedocola Dahal and Kim 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
43615	negative	0.9-1.2 µm	0.5-0.8 µm	rod-shaped
125439	negative
125438
125438	negative

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43615	1-2 mm	Orange	circular	5 days	R2A agar

Pigmentation

@ref	Production	Name
43615		Flexirubin-type

Culture and growth conditions

Culture medium

@ref	Name	Growth
43615	Reasoner's 2A agar (R2A)

Culture temp

@ref	Growth	Type	Temperature (°C)
43615	positive	growth	15-40
43615	positive	optimum	25-35
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH
43615	positive	optimum	7-8.5
43615	positive	growth	5.5-10.5

Physiology and metabolism

Oxygen tolerance

43615

Oxygen toleranceaerobe

Spore formation

43615

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43615	NaCl	positive	growth	0-2 %(w/v)
43615	NaCl	positive	optimum	0 %(w/v)

Observation

67770

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43615	16808 ChEBI	2-dehydro-D-gluconate	-	assimilation
43615	16193 ChEBI	3-hydroxybenzoate	-	assimilation
43615	37054 ChEBI	3-hydroxybutyrate	-	assimilation
43615	17879 ChEBI	4-hydroxybenzoate	-	assimilation
43615	355715 ChEBI	4-nitrophenyl beta-D-galactopyranoside	+	assimilation
43615	58143 ChEBI	5-dehydro-D-gluconate	-	assimilation
43615	17128 ChEBI	adipate	-	assimilation
43615		casein	+	hydrolysis
43615	17634 ChEBI	D-glucose	-	assimilation
43615	17634 ChEBI	D-glucose	+	assimilation
43615	16899 ChEBI	D-mannitol	-	assimilation
43615	16024 ChEBI	D-mannose	+	assimilation
43615	16988 ChEBI	D-ribose	+/-	assimilation
43615	17924 ChEBI	D-sorbitol	-	assimilation
43615	27689 ChEBI	decanoate	-	assimilation
43615		esculin ferric citrate	+	assimilation
43615	5291 ChEBI	gelatin	-	assimilation
43615	17234 ChEBI	glucose	-	fermentation
43615	28087 ChEBI	glycogen	-	assimilation
43615	17240 ChEBI	itaconate	-	assimilation
43615		L-alanine 4-nitroanilide	-	assimilation
43615	30849 ChEBI	L-arabinose	+	assimilation
43615	30849 ChEBI	L-arabinose	+/-	assimilation
43615	16467 ChEBI	L-arginine	-	assimilation
43615	18287 ChEBI	L-fucose	-	assimilation
43615	15971 ChEBI	L-histidine	-	assimilation
43615	38030 ChEBI	L-mannitol	-	assimilation
43615	17203 ChEBI	L-proline	-	assimilation
43615	62345 ChEBI	L-rhamnose	+	assimilation
43615	17115 ChEBI	L-serine	-	assimilation
43615	16828 ChEBI	L-tryptophan	-	assimilation
43615	24996 ChEBI	lactate	-	assimilation
43615	25115 ChEBI	malate	-	assimilation
43615	17306 ChEBI	maltose	+	assimilation
43615	28053 ChEBI	melibiose	+	assimilation
43615	17268 ChEBI	myo-inositol	-	assimilation
43615	506227 ChEBI	N-acetylglucosamine	+	assimilation
43615	17632 ChEBI	nitrate	-	reduction
43615	18401 ChEBI	phenylacetate	-	assimilation
43615	32032 ChEBI	potassium gluconate	-	assimilation
43615	17272 ChEBI	propionate	-	assimilation
43615	17814 ChEBI	salicin	+/-	assimilation
43615	32954 ChEBI	sodium acetate	-	assimilation
43615	53258 ChEBI	sodium citrate	-	assimilation
43615	62983 ChEBI	sodium malonate	-	assimilation
43615	28017 ChEBI	starch	-	hydrolysis
43615	9300 ChEBI	suberic acid	-	assimilation
43615	17992 ChEBI	sucrose	+	assimilation
43615	53426 ChEBI	tween 80	-	hydrolysis
43615	16199 ChEBI	urea	-	assimilation
43615	31011 ChEBI	valerate	-	assimilation

Antibiotic resistance

@ref	ChEBI	Metabolite
43615	28971	ampicillin
43615	17698	chloramphenicol
43615	27641	cycloheximide
43615	17833	gentamicin
43615	6104	kanamycin
43615	100147	nalidixic acid
43615	7507	neomycin
43615	28368	novobiocin
43615	17334	penicillin
43615	28077	rifampicin
43615	17076	streptomycin
43615	9332	sulfamethoxazole
43615	27902	tetracycline
43615	45924	trimethoprim

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43615	16136 ChEBI	hydrogen sulfide

Metabolite tests

@ref	Chebi-ID	Metabolite	Methylred-test
43615	17234 ChEBI	glucose	-

Enzymes

@ref	Value	Activity	Ec
43615	acid phosphatase	+	3.1.3.2
43615	alkaline phosphatase	+	3.1.3.1
43615	alpha-chymotrypsin	-	3.4.21.1
43615	alpha-fucosidase	+	3.2.1.51
43615	alpha-galactosidase	+	3.2.1.22
43615	alpha-glucosidase	+	3.2.1.20
43615	alpha-mannosidase	+	3.2.1.24
43615	beta-galactosidase	+	3.2.1.23
43615	beta-glucosidase	+	3.2.1.21
43615	beta-glucuronidase	-	3.2.1.31
43615	catalase	-	1.11.1.6
43615	cystine arylamidase	+	3.4.11.3
43615	cytochrome oxidase	+	1.9.3.1
43615	DNase	-
43615	esterase (C 4)	-
43615	esterase Lipase (C 8)	+/-
43615	leucine arylamidase	+	3.4.11.1
43615	lipase (C 14)	-
43615	N-acetyl-beta-glucosaminidase	+	3.2.1.52
43615	naphthol-AS-BI-phosphohydrolase	+
43615	trypsin	+/-	3.4.21.4
43615	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

43615

Fatty acid	Percentage
C15:0 anteiso	43.8
C16:0 iso	12.1
C16:0	10.5
C14:0 iso	7.2
C16:1ω11c	6.4
C15:0 iso	5.4
C14:0	5.3
C17:0 anteiso	3.5
C17:0 iso	1.4
C16:1ω7c-alcohol	1.3

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
43615	Soil	Hwaseong, Gyeonggi-Do	Republic of Korea	KOR	Asia
67770	Soil in Hwaseong	Gyeonggi-do	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence KT032154 (>99% sequence identity) for Niabella pedocola from Microbeatlas

Aquatic Samples	4
Soil Samples	16
Animal Samples	9
Plant Samples	10
Total Samples	39

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2104442v1 assembly for Niabella pedocola JCM 31011	contig	GCA_021044425	1752077.3	8065662421	1752077	72.46

Genome browser: GCA_021044425

16S sequences

@ref	Description	Accession	Database
43615	Niabella pedocola strain R384 16S ribosomal RNA gene, partial sequence	KT032154

GC content

@ref	GC-content (mol%)	Method
43615	44.7	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: Niabella pedocola JCM 31011
NCBI: GCA_021044425

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	73.20	no
125439	motility	BacteriaNetⓘ	yes	53.20	no
125439	gram_stain	BacteriaNetⓘ	negative	97.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	86.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Niabella pedocola JCM 31011
NCBI: GCA_021044425.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	92.33	no
125438	anaerobic	anaerobicⓘ	no	98.92	yes
125438	aerobic	aerobicⓘ	yes	88.26	yes
125438	spore-forming	spore-formingⓘ	no	87.98	no
125438	thermophilic	thermophileⓘ	no	97.33	yes
125438	flagellated	motile2+ⓘ	no	90.00	yes

Literature

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 )
#43615	Ram Hari Dahal, Jaisoo Kim: Niabella pedocola sp. nov., isolated from soil. IJSEM 66: 2650 - 2656 2016 ( DOI 10.1099/ijsem.0.001099 , PubMed 27098486 )
#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;
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#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 )

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Niabella pedocola (KEMB 9005-329, KACC 18454, JCM 31011)

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

Metabolite tests

Enzymes

Fatty acid profile?

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_021044425

16S sequences

GC content

Genome-based predictions

Predictions

Literature

References

BacDive

Help

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Fatty acid profile