Name: Nonlabens dokdonensis DSW-6
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5723

Type strain:

Species: Nonlabens dokdonensis

Strain Designation: DSW-6

Culture col. no.: DSM 17205, KCTC 12402

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 328515 (species)

SI-ID 289859

DSM 17205, KCTC 12402

Section

Nonlabens dokdonensis DSW-6 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sea water.

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	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Flavobacteriaceae*
	Genus	*Nonlabens*
	Species	**Nonlabens dokdonensis**
	Full Scientific Name (LPSN)	Nonlabens dokdonensis (Yoon et al. 2006) Yi and Chun 2012

	Synonym	Donghaeana dokdonensis
	Synonym	Persicivirga dokdonensis

Information on morphological and physiological properties Morphology

[Ref.: #31581]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.893

[Ref.: #31581]	Cell length	01-30 µm

[Ref.: #31581]	Cell width	0.4-0.6 µm

[Ref.: #31581]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #31581]	Motility	no
[Ref.: #67771]	Motility	no

[Ref.: #31581]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6815]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #6815]

Culture medium growth

[Ref.: #6815]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6815]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #6815]	growth	25 °C
[Ref.: #31581]	growth	04-32 °C
[Ref.: #31581]	optimum	25 °C
[Ref.: #67771]	growth	25 °C

[Ref.: #6815]	Temperature range	mesophilic
[Ref.: #31581]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31581]			optimum	07-08
[Ref.: #31581]			growth	5.5-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31581]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #31581]	Ability of spore formation	no
[Ref.: #67771]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.996

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31581]		NaCl		growth	02-08	%
[Ref.: #31581]		NaCl		optimum	2	%

[Ref.: #31581]	Observation	aggregates in chains
[Ref.: #67771]	Observation	quinones: MK-6

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31581]	esculin ChEBI	+	hydrolysis
[Ref.: #31581]	tween 20 ChEBI	+	carbon source
[Ref.: #31581]	tween 40 ChEBI	+	carbon source

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

[Ref.: #6815]	Sample type/isolated from	sea water
[Ref.: #6815]	Geographic location (country and/or sea, region)	Dokdo
[Ref.: #6815]	Country	Republic of Korea
[Ref.: #6815]	Country ISO 3 Code	KOR
[Ref.: #6815]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From sea water
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Marine

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ017065 (>99% sequence identity) for Nonlabens dokdonensis subclade from Microbeatlas

Aquatic Samples	1624
Soil Samples	34
Animal Samples	1018
Plant Samples	14
Total Samples	2690

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

[Ref.: #6815]

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.: #6815]	Donghaeana dokdonensis strain DSW-6 16S ribosomal RNA gene, partial sequence	DQ017065	1481	ENA	592029 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Nonlabens dokdonensis DSM 17205	GCA_003254015	scaffold	GenBank	328515 tax ID	*
[Ref.: #66792]	Nonlabens dokdonensis DSW-6	GCA_000332115	complete	GenBank	592029 tax ID	*
[Ref.: #66792]	Nonlabens dokdonensis DSW-6	592029.3	complete	PATRIC	592029 tax ID	*
[Ref.: #66792]	Nonlabens dokdonensis strain DSM 17205	328515.4	wgs	PATRIC	328515 tax ID	*
[Ref.: #66792]	Nonlabens dokdonensis DSM 17205	2593339282	draft	JGI IMG/M	328515 tax ID	*
[Ref.: #66792]	Nonlabens dokdonensis DSW-6	2540341128	complete	JGI IMG/M	592029 tax ID	*

[Ref.: #6815]

GC-content

36.9 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: Nonlabens dokdonensis DSW-6 PATRIC: 592029.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nonlabens dokdonensis DSW-6 DSW-6 NCBI: GCA_000332115.1
[Ref.: #69480]	motile	no	88.563	yes
[Ref.: #69480]	flagellated	no	95.7	no
[Ref.: #69480]	gram-positive	no	97.517	no
[Ref.: #69480]	anaerobic	no	99.455	yes
[Ref.: #69480]	aerobic	yes	90.572	no
[Ref.: #69480]	halophile	no	55.612	no
[Ref.: #69480]	spore-forming	no	93.792	no
[Ref.: #69480]	thermophile	no	99.192	yes
[Ref.: #69480]	glucose-util	yes	81.64	no
[Ref.: #69480]	glucose-ferment	no	86.793	no

Availability in culture collections External links

[Ref.: #6815]

Culture collection no.

DSM 17205, KCTC 12402

[Ref.: #75203]

SI-ID 289859

Literature:

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

	Title	Authors	Journal	DOI	Year
Metabolism	Crystal structure of 1'-OH-carotenoid 3,4-desaturase from Nonlabens dokdonensis DSW-6.	Ahn JW, Kim KJ	Enzyme Microb Technol	10.1016/j.enzmictec.2015.05.005	2015	*
Genetics	Genomic makeup of the marine flavobacterium Nonlabens (Donghaeana) dokdonensis and identification of a novel class of rhodopsins.	Kwon SK, Kim BK, Song JY, Kwak MJ, Lee CH, Yoon JH, Oh TK, Kim JF	Genome Biol Evol	10.1093/gbe/evs134	2013	*
Phylogeny	Spongiimonas flava gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from an unidentified marine sponge.	Yoon J, Jang JH, Kasai H	Antonie Van Leeuwenhoek	10.1007/s10482-012-9846-4	2012	*
Phylogeny	Reclassification of Donghaeana dokdonensis Yoon et al. 2006 as Persicivirga dokdonensis comb. nov. and emended descriptions of the genus Persicivirga and of Persicivirga xylanidelens O'Sullivan et al. 2006.	Nedashkovskaya OI, Kwon KK, Kim SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.005116-0	2009	*
Phylogeny	Biosynthesis of bile acids in a variety of marine bacterial taxa.	Kim D, Lee JS, Kim J, Kang SJ, Yoon JH, Kim WG, Lee CH	J Microbiol Biotechnol		2007	*
Phylogeny	Donghaeana dokdonensis gen. nov., sp. nov., isolated from sea water.	Yoon JH, Kang SJ, Lee CH, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.63847-0	2006	*
	Crystal structure of geranylgeranyl pyrophosphate synthase (crtE) from Nonlabens dokdonensis DSW-6.	Kim S, Kim EJ, Park JB, Kim SW, Kim KJ	Biochem Biophys Res Commun	10.1016/j.bbrc.2019.08.071	2019	*

References

#6815

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17205

#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 )

#31581

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 #27870 (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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

#75203

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-ID289859.1 )

#27870

IJSEM 187 2006 ( DOI 10.1099/ijs.0.63847-0 , PubMed 16403885 )

* These data were automatically processed and therefore are not curated

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Nonlabens dokdonensis DSW-6

Nonlabens dokdonensis DSW-6 DSW-6

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