Name: Niabella pedocola R384
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140823

Type strain:

Species: Niabella pedocola

Strain Designation: R384

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

Strain history: J. Kim; Kyonggi Univ., South Korea; R384.

NCBI tax ID(s): 1752077 (species)

Section

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

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

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	*Chitinophagia*
	Order	*Chitinophagales*
	Family	*Chitinophagaceae*
	Genus	*Niabella*
	Species	**Niabella pedocola**
	Full Scientific Name (LPSN)	Niabella pedocola Dahal and Kim 2016

Information on morphological and physiological properties Morphology

[Ref.: #43615]	Gram stain	negative

[Ref.: #43615]	Cell length	0.9-1.2 µm

[Ref.: #43615]	Cell width	0.5-0.8 µm

[Ref.: #43615]	Cell shape	rod-shaped

[Ref.: #43615]	Motility	no

[Ref.: #43615]	Colony size	1-2 mm
[Ref.: #43615]	Colony color	Orange
[Ref.: #43615]	Colony shape	circular
[Ref.: #43615]	Incubation period	5 days
[Ref.: #43615]	Cultivation medium used	R2A agar

[Ref.: #43615]	Pigment production	yes
[Ref.: #43615]	Pigment name	Flexirubin-type

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43615]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #43615]

Culture medium growth

		Temperature
[Ref.: #43615]	growth	15-40 °C
[Ref.: #43615]	optimum	25-35 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #43615]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43615]			optimum	7-8.5
[Ref.: #43615]			growth	5.5-10.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43615]

Oxygen tolerance

aerobe

[Ref.: #43615]

Ability of spore formation

[Ref.: #43615]

Halophily / tolerance level

non-halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43615]		NaCl		growth	0-2	%(w/v)
[Ref.: #43615]		NaCl		optimum	0	%(w/v)

[Ref.: #67770]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43615]	2-dehydro-D-gluconate ChEBI	-	assimilation
[Ref.: #43615]	3-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #43615]	3-hydroxybutyrate ChEBI	-	assimilation
[Ref.: #43615]	4-hydroxybenzoate ChEBI	-	assimilation
[Ref.: #43615]	4-nitrophenyl beta-D-galactopyranoside ChEBI	+	assimilation
[Ref.: #43615]	5-dehydro-D-gluconate ChEBI	-	assimilation
[Ref.: #43615]	adipate ChEBI	-	assimilation
[Ref.: #43615]	casein	+	hydrolysis
[Ref.: #43615]	D-glucose ChEBI	-	assimilation
[Ref.: #43615]	D-glucose ChEBI	+	assimilation
[Ref.: #43615]	D-mannitol ChEBI	-	assimilation
[Ref.: #43615]	D-mannose ChEBI	+	assimilation
[Ref.: #43615]	D-ribose ChEBI	+/-	assimilation
[Ref.: #43615]	D-sorbitol ChEBI	-	assimilation
[Ref.: #43615]	decanoate ChEBI	-	assimilation
[Ref.: #43615]	esculin ferric citrate	+	assimilation
[Ref.: #43615]	gelatin ChEBI	-	assimilation
[Ref.: #43615]	glucose ChEBI	-	fermentation
[Ref.: #43615]	glycogen ChEBI	-	assimilation
[Ref.: #43615]	itaconate ChEBI	-	assimilation
[Ref.: #43615]	L-alanine 4-nitroanilide	-	assimilation
[Ref.: #43615]	L-arabinose ChEBI	+	assimilation
[Ref.: #43615]	L-arabinose ChEBI	+/-	assimilation
[Ref.: #43615]	L-arginine ChEBI	-	assimilation
[Ref.: #43615]	L-fucose ChEBI	-	assimilation
[Ref.: #43615]	L-histidine ChEBI	-	assimilation
[Ref.: #43615]	L-mannitol ChEBI	-	assimilation
[Ref.: #43615]	L-proline ChEBI	-	assimilation
[Ref.: #43615]	L-rhamnose ChEBI	+	assimilation
[Ref.: #43615]	L-serine ChEBI	-	assimilation
[Ref.: #43615]	L-tryptophan ChEBI	-	assimilation
[Ref.: #43615]	lactate ChEBI	-	assimilation
[Ref.: #43615]	malate ChEBI	-	assimilation
[Ref.: #43615]	maltose ChEBI	+	assimilation
[Ref.: #43615]	melibiose ChEBI	+	assimilation
[Ref.: #43615]	myo-inositol ChEBI	-	assimilation
[Ref.: #43615]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #43615]	nitrate ChEBI	-	reduction
[Ref.: #43615]	phenylacetate ChEBI	-	assimilation
[Ref.: #43615]	potassium gluconate ChEBI	-	assimilation
[Ref.: #43615]	propionate ChEBI	-	assimilation
[Ref.: #43615]	salicin ChEBI	+/-	assimilation
[Ref.: #43615]	sodium acetate ChEBI	-	assimilation
[Ref.: #43615]	sodium citrate ChEBI	-	assimilation
[Ref.: #43615]	sodium malonate ChEBI	-	assimilation
[Ref.: #43615]	starch ChEBI	-	hydrolysis
[Ref.: #43615]	suberic acid ChEBI	-	assimilation
[Ref.: #43615]	sucrose ChEBI	+	assimilation
[Ref.: #43615]	tween 80 ChEBI	-	hydrolysis
[Ref.: #43615]	urea ChEBI	-	assimilation
[Ref.: #43615]	valerate ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #43615]	ampicillin ChEBI				yes
[Ref.: #43615]	chloramphenicol ChEBI				yes	100	µg (disc)
[Ref.: #43615]	cycloheximide ChEBI				yes	30	µg (disc)
[Ref.: #43615]	gentamicin ChEBI				yes	10	µg (disc)
[Ref.: #43615]	kanamycin ChEBI				yes	30	µg (disc)
[Ref.: #43615]	nalidixic acid ChEBI	yes	30	µg (disc)
[Ref.: #43615]	neomycin ChEBI	yes
[Ref.: #43615]	novobiocin ChEBI				yes	30	µg (disc)
[Ref.: #43615]	penicillin ChEBI				yes
[Ref.: #43615]	rifampicin ChEBI	yes
[Ref.: #43615]	streptomycin ChEBI	yes
[Ref.: #43615]	sulfamethoxazole ChEBI				yes
[Ref.: #43615]	tetracycline ChEBI	yes
[Ref.: #43615]	trimethoprim ChEBI				yes
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43615]		hydrogen sulfide ChEBI	no

	Physiological tests	Metabolite	Methylred-test
[Ref.: #43615]		glucose ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #43615]	acid phosphatase	+	3.1.3.2
[Ref.: #43615]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43615]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #43615]	alpha-fucosidase	+	3.2.1.51
[Ref.: #43615]	alpha-galactosidase	+	3.2.1.22
[Ref.: #43615]	alpha-glucosidase	+	3.2.1.20
[Ref.: #43615]	alpha-mannosidase	+	3.2.1.24
[Ref.: #43615]	beta-galactosidase	+	3.2.1.23
[Ref.: #43615]	beta-glucosidase	+	3.2.1.21
[Ref.: #43615]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43615]	catalase	-	1.11.1.6
[Ref.: #43615]	cystine arylamidase	+	3.4.11.3
[Ref.: #43615]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43615]	DNase	-
[Ref.: #43615]	esterase (C 4)	-
[Ref.: #43615]	esterase Lipase (C 8)	+/-
[Ref.: #43615]	leucine arylamidase	+	3.4.11.1
[Ref.: #43615]	lipase (C 14)	-
[Ref.: #43615]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #43615]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43615]	trypsin	+/-	3.4.21.4
[Ref.: #43615]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[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

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

[Ref.: #43615]	Sample type/isolated from	Soil
[Ref.: #43615]	Geographic location (country and/or sea, region)	Hwaseong, Gyeonggi-Do
[Ref.: #43615]	Country	Republic of Korea
[Ref.: #43615]	Country ISO 3 Code	KOR
[Ref.: #43615]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil in Hwaseong
[Ref.: #67770]	Geographic location (country and/or sea, region)	Gyeonggi-do
[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 KT032154 (>99% sequence identity) for Niabella pedocola from Microbeatlas

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

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.: #43615]	16S rRNA gene sequence	KT032154		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Niabella pedocola JCM 31011	GCA_021044425	contig	GenBank	1752077 tax ID	*

[Ref.: #43615]

GC-content

44.7 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Niabella pedocola JCM 31011 NCBI: GCA_021044425.1
[Ref.: #69480]	flagellated	no	98.087	no
[Ref.: #69480]	gram-positive	no	97.766	yes
[Ref.: #69480]	anaerobic	no	99.686	yes
[Ref.: #69480]	aerobic	yes	90.452	no
[Ref.: #69480]	halophile	no	96.931	no
[Ref.: #69480]	spore-forming	no	94.472	no
[Ref.: #69480]	motile	no	93.926	no
[Ref.: #69480]	thermophile	no	98.209	no
[Ref.: #69480]	glucose-util	yes	84.701	no
[Ref.: #69480]	glucose-ferment	no	89.786	yes

Availability in culture collections External links

[Ref.: #43615]

Culture collection no.

KEMB 9005-329, KACC 18454, JCM 31011

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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

* These data were automatically processed and therefore are not curated

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Niabella pedocola JCM 31011

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