Name: Niabella soli JS13-8
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17759

Type strain:

Species: Niabella soli

Strain Designation: JS13-8

Culture col. no.: DSM 19437, KACC 12604

Strain history: <- S.-W. Kwon, KACC; JS13-8 <- H.-Y. Weon, Natl. Inst. Agricult. Sci. and Technol., Suwon, Korea

NCBI tax ID(s): 929713 (strain), 446683 (species)

SI-ID 398756

DSM 19437

Section

Niabella soli JS13-8 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

Gram-negative
rod-shaped
aerobe
mesophilic
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 soli**
	Full Scientific Name (LPSN)	Niabella soli Weon et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32318]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #32318]	Cell length	1.1 µm

[Ref.: #32318]	Cell width	0.6 µm

[Ref.: #32318]	Cell shape	rod-shaped

[Ref.: #32318]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %90.983

[Ref.: #32318]

Pigment production

yes

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8016]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #8016]

Culture medium growth

[Ref.: #8016]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8016]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #8016]	growth	37 °C
[Ref.: #32318]	growth	15-35 °C
[Ref.: #32318]	optimum	30 °C

[Ref.: #8016]	Temperature range	mesophilic
[Ref.: #32318]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32318]			optimum	6.5
[Ref.: #32318]			growth	05-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32318]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.998

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32318]		NaCl		growth	0-1	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32318]	arabinose ChEBI	+	carbon source
[Ref.: #32318]	esculin ChEBI	+	hydrolysis
[Ref.: #32318]	glucose ChEBI	+	carbon source
[Ref.: #32318]	maltose ChEBI	+	carbon source
[Ref.: #32318]	mannose ChEBI	+	carbon source
[Ref.: #32318]	melibiose ChEBI	+	carbon source
[Ref.: #32318]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #32318]	rhamnose ChEBI	+	carbon source
[Ref.: #32318]	salicin ChEBI	+	carbon source
[Ref.: #32318]	sucrose ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #32318]	acid phosphatase	+	3.1.3.2
[Ref.: #32318]	alkaline phosphatase	+	3.1.3.1
[Ref.: #32318]	alpha-galactosidase	+	3.2.1.22

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	lactate fermentation	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	degradation of pentoses	75	21 of 28
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	d-xylose degradation	72.73	8 of 11
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	lysine metabolism	64.29	27 of 42
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	tryptophan metabolism	63.16	24 of 38
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	degradation of sugar acids	60	15 of 25
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	alanine metabolism	58.62	17 of 29
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	aspartate and asparagine metabolism	55.56	5 of 9
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	phenylpropanoid biosynthesis	53.85	7 of 13
[Ref.: #66794]	vitamin B1 metabolism	53.85	7 of 13
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	daunorubicin biosynthesis	44.44	4 of 9
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	oxidative phosphorylation	32.97	30 of 91
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #8016]	Sample type/isolated from	soil
[Ref.: #8016]	Geographic location (country and/or sea, region)	Jeju Island
[Ref.: #8016]	Country	Republic of Korea
[Ref.: #8016]	Country ISO 3 Code	KOR
[Ref.: #8016]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EF592608 (>99% sequence identity) for Niabella soli subclade from Microbeatlas

Aquatic Samples	630
Soil Samples	564
Animal Samples	203
Plant Samples	284
Total Samples	1681

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #8016]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #8016]	Niabella soli strain JS13-8 16S ribosomal RNA gene, partial sequence	EF592608	1390	ENA	929713 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Niabella soli DSM 19437	GCA_000243115	contig	GenBank	929713 tax ID	*
[Ref.: #66792]	Niabella soli DSM 19437	929713.3	wgs	PATRIC	929713 tax ID	*
[Ref.: #66792]	Niabella soli JS13-8, DSM 19437	2506783006	complete	JGI IMG/M	929713 tax ID	*

[Ref.: #8016]	GC-content	45.0 mol%
[Ref.: #32318]	GC-content	45 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Niabella soli DSM 19437 JS13-8 NCBI: GCA_000243115.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Niabella soli DSM 19437 JS13-8 NCBI: GCA_000243115.3
[Ref.: #69480]	motile	no	95.614	yes
[Ref.: #69480]	flagellated	no	97.994	yes
[Ref.: #69480]	gram-positive	no	97.383	yes
[Ref.: #69480]	anaerobic	no	99.554	yes
[Ref.: #69480]	aerobic	yes	89.861	no
[Ref.: #69480]	halophile	no	96.215	yes
[Ref.: #69480]	spore-forming	no	95.277	no
[Ref.: #69480]	thermophile	no	92.931	yes
[Ref.: #69480]	glucose-util	yes	88.78	no
[Ref.: #69480]	glucose-ferment	no	87.098	no

Availability in culture collections External links

[Ref.: #8016]

Culture collection no.

DSM 19437, KACC 12604

[Ref.: #86750]

SI-ID 398756

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Niabella hibiscisoli sp. nov., isolated from soil of a Rose of Sharon garden.	Ngo HTT, Trinh H, Yan ZF, Moya G, Kook M, Yi TH	Int J Syst Evol Microbiol	10.1099/ijsem.0.001595	2017	*
Phylogeny	Niabella ginsenosidivorans sp. nov., isolated from compost.	Yi KJ, Im WT, Kim DW, Liu QM, Kim SK	J Microbiol	10.1007/s12275-015-5463-z	2015	*
Genetics	Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T)).	Anderson I, Munk C, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin L, Pitluck S, Liolios K, Mavromatis K, Pagani I, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Tindall BJ, Goker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Ivanova N	Stand Genomic Sci	10.4056/sigs.3117229	2012	*
Phylogeny	Niabella yanshanensis sp. nov., isolated from the soybean rhizosphere.	Wang H, Zhang YZ, Man CX, Chen WF, Sui XH, Li Y, Zhang XX, Chen WX	Int J Syst Evol Microbiol	10.1099/ijs.0.010447-0	2009	*
Phylogeny	Niabella ginsengisoli sp. nov., isolated from soil cultivated with Korean ginseng.	Weon HY, Yoo SH, Kim BY, Son JA, Kim YJ, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijs.0.004333-0	2009	*
Phylogeny	Niabella soli sp. nov., isolated from soil from Jeju Island, Korea.	Weon HY, Kim BY, Joa JH, Kwon SW, Kim WG, Koo BS	Int J Syst Evol Microbiol	10.1099/ijs.0.65304-0	2008	*

References

#8016

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19437

#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 )

#32318

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 #28554 (see below)

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#86750

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-ID398756.1 )

#28554

IJSEM 467 2008 ( DOI 10.1099/ijs.0.65304-0 , PubMed 18218950 )

* These data were automatically processed and therefore are not curated

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Niabella soli DSM 19437 JS13-8

Niabella soli DSM 19437 JS13-8

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