Name: Niabella aurantiaca R2A15-11
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17758

Type strain:

Species: Niabella aurantiaca

Strain Designation: R2A15-11

Culture col. no.: DSM 17617, CIP 109580, KACC 11698

Strain history: CIP <- 2007, DSMZ <- KACC <- Korea: strain R2A15-11

NCBI tax ID(s): 1122605 (strain), 379900 (species)

SI-ID 297283

DSM 17617, KACC 11698, CIP 109580

Special Collections

Section

Niabella aurantiaca R2A15-11 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from greenhouse soil.

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 aurantiaca**
	Full Scientific Name (LPSN)	Niabella aurantiaca Kim et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #31897]	Gram stain	negative
[Ref.: #116554]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %92.615

[Ref.: #31897]	Cell length	1.25 µm

[Ref.: #31897]	Cell width	0.8 µm

[Ref.: #31897]	Cell shape	rod-shaped
[Ref.: #116554]	Cell shape	oval-shaped

[Ref.: #31897]	Motility	no
[Ref.: #116554]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %92

[Ref.: #31897]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7090]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7090]

Culture medium growth

[Ref.: #7090]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7090]

Culture medium composition

expand / minimize

[Ref.: #33310]

Culture medium

MEDIUM 372 - for Aquabacterium

[Ref.: #33310]

Culture medium growth

[Ref.: #33310]

Culture medium composition

expand / minimize

[Ref.: #116554]

Culture medium

CIP Medium 372

[Ref.: #116554]

Culture medium growth

[Ref.: #116554]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #7090]	growth	28 °C
[Ref.: #31897]	growth	10-35 °C
[Ref.: #31897]	optimum	27.5 °C
[Ref.: #33310]	growth	25 °C

	pH	Kind of pH		pH
[Ref.: #31897]			optimum	6.5
[Ref.: #31897]			growth	5.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31897]	Oxygen tolerance	aerobe
[Ref.: #116554]	Oxygen tolerance	obligate aerobe

[Ref.: #31897]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31897]		NaCl		growth	0-3	%
[Ref.: #31897]		NaCl		optimum	1.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31897]	esculin ChEBI	+	hydrolysis
[Ref.: #68371]	esculin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31897]	maltose ChEBI	+	carbon source
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31897]	melibiose ChEBI	+	carbon source
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #116554]	nitrate ChEBI	-	reduction
[Ref.: #116554]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31897]	rhamnose ChEBI	+	carbon source
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31897]	salicin ChEBI	+	carbon source
[Ref.: #31897]	sucrose ChEBI	+	carbon source
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #31897]		indole ChEBI	yes
[Ref.: #116554]		indole ChEBI	yes

	Physiological tests	Metabolite	Indole test
[Ref.: #31897]		indole ChEBI	+

	Enzyme	Enzyme activity	EC number
[Ref.: #31897]	acid phosphatase	+	3.1.3.2
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #31897]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	+	3.2.1.51	* from API zym
[Ref.: #31897]	alpha-galactosidase	+	3.2.1.22
[Ref.: #68382]	alpha-galactosidase	+	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	+	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #31897]	catalase	+	1.11.1.6
[Ref.: #116554]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #31897]	gelatinase	+
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #116554]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #116554]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #116554]	11603	not determinedn.d.	-	-	+/-	+/-	-	+/-	-	-	-	+/-	+/-	+/-	+/-	-	-	-	-	-	-	+/-	+/-	+/-	+/-	+/-	+	+/-	+/-	+/-	+/-	+/-	+/-	+/-	-	-	+/-	+/-	-	-	+/-	+/-	+/-	-	-	+/-	-	-	-	-	+/-

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #116554]	11973	-	+	+	+	-	+	-	-	-	-	+	+	+	+	-	+	+	+	+	+

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

[Ref.: #7090]	Sample type/isolated from	greenhouse soil
[Ref.: #7090]	Geographic location (country and/or sea, region)	Yeoju region
[Ref.: #7090]	Country	Republic of Korea
[Ref.: #7090]	Country ISO 3 Code	KOR
[Ref.: #7090]	Continent	Asia

[Ref.: #116554]	Sample type/isolated from	Environment, Soil, greenhouse
[Ref.: #116554]	Geographic location (country and/or sea, region)	Yeoju region
[Ref.: #116554]	Country	Republic of Korea
[Ref.: #116554]	Country ISO 3 Code	KOR
[Ref.: #116554]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Greenhouse
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ457019 (>99% sequence identity) for Niabella aurantiaca subclade from Microbeatlas

Aquatic Samples	291
Soil Samples	340
Animal Samples	214
Plant Samples	164
Total Samples	1009

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

[Ref.: #7090]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #116554]	Biosafety level	1	Risk group (French classification)

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.: #7090]	Niabella aurantiaca strain R2A15-11 16S ribosomal RNA gene, partial sequence	DQ457019	1465	GenBank ENA	379900 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Niabella aurantiaca DSM 17617	GCA_000374125	scaffold	GenBank ENA	1122605 tax ID	*
[Ref.: #66792]	Niabella aurantiaca DSM 17617	1122605.3	wgs	PATRIC	1122605 tax ID	*
[Ref.: #66792]	Niabella aurantiaca DSM 17617	2515154175	draft	JGI IMG/M	1122605 tax ID	*

[Ref.: #7090]	GC-content	45.0 mol%
[Ref.: #31897]	GC-content	45 mol%
[Ref.: #7090]	GC-content	48.6 mol%	sequence analysis

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Niabella aurantiaca DSM 17617 DSM 17617 NCBI: GCA_000374125.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Niabella aurantiaca DSM 17617 DSM 17617 NCBI: GCA_000374125.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	92.615	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.666	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	87.604	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	89.413	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	98.426	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	92	yes

Availability in culture collections External links

[Ref.: #7090]

Culture collection no.

DSM 17617, CIP 109580, KACC 11698

[Ref.: #86749]

SI-ID 297283

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Niabella aquatica sp. nov., isolated from lake water.	Siddiqi MZ, Im WT	Int J Syst Evol Microbiol	10.1099/ijsem.0.001053	2016	*
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	Sediminibacterium salmoneum gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from sediment of a eutrophic reservoir.	Qu JH, Yuan HL	Int J Syst Evol Microbiol	10.1099/ijs.0.65514-0	2008	*
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	*
Phylogeny	Niabella aurantiaca gen. nov., sp. nov., isolated from a greenhouse soil in Korea.	Kim BY, Weon HY, Yoo SH, Hong SB, Kwon SW, Stackebrandt E, Go SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.64614-0	2007	*

References

#7090

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17617

#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 )

#31897

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 #28155 (see below)

#33310 ; Curators of the CIP;

#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) .

#68371

Automatically annotated from API 50CH acid .

#68382

Automatically annotated from API zym .

#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 )

#86749

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-ID297283.1 )

#116554 Collection of Institut Pasteur ; Curators of the CIP; CIP 109580

#28155

IJSEM 538 2007 ( DOI 10.1099/ijs.0.64614-0 , PubMed 17329780 )

* These data were automatically processed and therefore are not curated

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Niabella aurantiaca DSM 17617 DSM 17617

Niabella aurantiaca DSM 17617 DSM 17617

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