Name: Dyadobacter ginsengisoli DSM 21015
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 3778

Type strain:

Species: Dyadobacter ginsengisoli

Culture col. no.: DSM 21015, KCTC 12589, LMG 23409, Gsoil 043

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 1121484 (strain), 363850 (species)

SI-ID 289786

LMG 23409, KCTC 12589, DSM 21015

Section

Dyadobacter ginsengisoli DSM 21015 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil from ginseng field.

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	*Cytophagia*
	Order	*Cytophagales*
	Family	*Spirosomataceae*
	Genus	*Dyadobacter*
	Species	**Dyadobacter ginsengisoli**
	Full Scientific Name (LPSN)	Dyadobacter ginsengisoli Liu et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #31804]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative

[Ref.: #31804]	Cell length	03-06 µm

[Ref.: #31804]	Cell width	0.6-0.8 µm

[Ref.: #31804]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #31804]	Motility	no
[Ref.: #67771]	Motility	no

[Ref.: #31804]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15427]

Culture medium

REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)

[Ref.: #15427]

Culture medium growth

[Ref.: #15427]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15427]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #15427]	growth	28 °C
[Ref.: #31804]	growth	04-30 °C
[Ref.: #31804]	optimum	30 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #15427]	Temperature range	mesophilic
[Ref.: #31804]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31804]			optimum	7
[Ref.: #31804]			growth	5.5-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31804]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #31804]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31804]		NaCl		growth	0-1	%

[Ref.: #31804]	Observation	aggregates in chains
[Ref.: #67771]	Observation	quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31804]	lactose ChEBI	+	carbon source
[Ref.: #31804]	maltose ChEBI	+	carbon source
[Ref.: #31804]	melibiose ChEBI	+	carbon source
[Ref.: #31804]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #31804]	nitrate ChEBI	+	reduction
[Ref.: #31804]	rhamnose ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31804]		catalase	+	1.11.1.6
[Ref.: #31804]		cytochrome oxidase	+	1.9.3.1

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

[Ref.: #15427]	Sample type/isolated from	soil from ginseng field
[Ref.: #15427]	Geographic location (country and/or sea, region)	Pocheon province
[Ref.: #15427]	Country	Republic of Korea
[Ref.: #15427]	Country ISO 3 Code	KOR
[Ref.: #15427]	Continent	Asia

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

Isolation sources categories

#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB245369 (>99% sequence identity) for Dyadobacter ginsengisoli subclade from Microbeatlas

Aquatic Samples	18
Soil Samples	187
Animal Samples	9
Plant Samples	266
Total Samples	480

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

[Ref.: #15427]

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.: #15427]	Dyadobacter ginsengisoli gene for 16S rRNA, partial sequence, strain: Gsoil 043	AB245369	1451	ENA	363850 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Dyadobacter ginsengisoli DSM 21015	2574179707	draft	JGI IMG/M	1121484 tax ID	*

[Ref.: #31804]	GC-content	48 mol%
[Ref.: #15427]	GC-content	49.0 mol%	sequence analysis
[Ref.: #67771]	GC-content	48.0 mol%

Availability in culture collections External links

[Ref.: #15427]

Culture collection no.

DSM 21015, KCTC 12589, LMG 23409, Gsoil 043

[Ref.: #73290]

SI-ID 289786

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Dyadobacter sandarakinus sp. nov., isolated from Arctic tundra soil, and emended descriptions of Dyadobacter alkalitolerans, Dyadobacter koreensis and Dyadobacter psychrophilus.	Zhang Y, Peng X, Qin K, Liu J, Xu Q, Niu J, Zheng Y, Peng F	Int J Syst Evol Microbiol	10.1099/ijsem.0.005103	2021	*
Phylogeny	Dyadobacter jejuensis sp. nov., isolated from seawater.	Chun J, Kang JY, Joung Y, Kim H, Joh K, Jahng KY	Int J Syst Evol Microbiol	10.1099/ijs.0.043620-0	2012	*
Phylogeny	Dyadobacter soli sp. nov., a starch-degrading bacterium isolated from farm soil.	Lee M, Woo SG, Park J, Yoo SA	Int J Syst Evol Microbiol	10.1099/ijs.0.019653-0	2009	*
Phylogeny	Dyadobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from soil.	Zhang DC, Liu HC, Xin YH, Zhou YG, Schinner F, Margesin R	Int J Syst Evol Microbiol	10.1099/ijs.0.017236-0	2009	*
Phylogeny	Dyadobacter ginsengisoli sp. nov., isolated from soil of a ginseng field.	Liu QM, Im WT, Lee M, Yang DC, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.64322-0	2006	*

References

#15427

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21015

#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 )

#31804

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 #28073 (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 .

#73290

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-ID289786.1 )

#28073

IJSEM 1939 2006 ( DOI 10.1099/ijs.0.64322-0 , PubMed 16902034 )

* These data were automatically processed and therefore are not curated

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