Dokdonella koreensis (DSM 17203, KCTC 12396, DS-123)

Name: Dokdonella koreensis (DSM 17203, KCTC 12396, DS-123)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17450

Type strain

Strain Designation DS-123

Culture col. no. DSM 17203 KCTC 12396 DS-123

NCBI tax ID(s) 323415

Special Collections DSMZ KCTC Literature strains

History <- J.-H. Yoon; DS-123 <- JH Yoon, KRIBB

Links

Dokdonella koreensis DS-123 is an aerobe, Gram-negative, motile bacterium that was isolated from soil.

Gram-negative motile rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 289858

DSM 17203,KCTC 12396

@ref 20215

Last LPSN update 2026-02-09 11:22:13

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Rhodanobacteraceae

Genus Dokdonella

Species Dokdonella koreensis

Full scientific name Dokdonella koreensis Yoon et al. 2006

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31556	negative	01-02 µm	0.3-0.5 µm	rod-shaped
67771	negative
125438	negative				100
125439	negative				94.7

Pigmentation

31556

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6813	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)		Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
6813	positive	growth	28
31556	positive	growth	10-39
31556	positive	optimum	30
67771	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
31556	positive	optimum	6.5
31556	positive	growth	05-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31556	aerobe
67771	aerobe
125439	obligate aerobe	99.8

Spore formation

@ref	Spore formation	Confidence
31556
125438		93.786
125439		94.1

Observation

@ref	Observation
31556	aggregates in chains
67771	quinones: Q-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31556	15361 ChEBI	pyruvate	+	carbon source

Enzymes

@ref	Value	Activity	Ec
31556	catalase	+	1.11.1.6
31556	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6813	soil	Dokdo	Republic of Korea	KOR	Asia
67771	From soil	Dokdo	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence AY987368 (>99% sequence identity) for Dokdonella koreensis subclade from Microbeatlas

Aquatic Samples	1601
Soil Samples	533
Animal Samples	536
Plant Samples	82
Total Samples	2752

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6813	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM163277v1 assembly for Dokdonella koreensis DS-123	complete	GCA_001632775	1300342.5	2687453174	1300342	98.62

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6813	Dokdonella koreensis strain DS-123 16S ribosomal RNA gene, partial sequence	AY987368	1494		323415

GC content

@ref	GC-content (mol%)
6813	71.0
31556	71

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Dokdonella koreensis DS-123
PATRIC: 1300342.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	94.10	no
125439	motility	BacteriaNetⓘ	yes	75.50	no
125439	gram_stain	BacteriaNetⓘ	negative	94.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Dokdonella koreensis DS-123 DS-123
NCBI: GCA_001632775.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	yes
125438	anaerobic	anaerobicⓘ	no	97.22	yes
125438	aerobic	aerobicⓘ	yes	81.80	no
125438	spore-forming	spore-formingⓘ	no	93.79	yes
125438	thermophilic	thermophileⓘ	no	96.39	yes
125438	flagellated	motile2+ⓘ	no	63.74	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Dokdonella immobilis sp. nov., isolated from a batch reactor for the treatment of triphenylmethane dye effluent.	Liu Y, Jin JH, Liu HC, Liu ZP	Int J Syst Evol Microbiol	10.1099/ijs.0.042002-0	2012
Phylogeny	Metallibacterium scheffleri gen. nov., sp. nov., an alkalinizing gammaproteobacterium isolated from an acidic biofilm.	Ziegler S, Waidner B, Itoh T, Schumann P, Spring S, Gescher J	Int J Syst Evol Microbiol	10.1099/ijs.0.042986-0	2012
Phylogeny	Dokdonella ginsengisoli sp. nov., isolated from soil from a ginseng field, and emended description of the genus Dokdonella.	Ten LN, Jung HM, Im WT, Oh HW, Yang DC, Yoo SA, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.004945-0	2009
Phylogeny	Dokdonella soli sp. nov., a gammaproteobacterium isolated from soil.	Yoo SH, Weon HY, Anandham R, Kim BY, Hong SB, Jeon YA, Koo BS, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijs.0.005348-0	2009
Phylogeny	Dokdonella koreensis gen. nov., sp. nov., isolated from soil.	Yoon JH, Kang SJ, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.63802-0	2006

References

#6813	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17203
#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 )
#27846	IJSEM 145 2006 ( DOI 10.1099/ijs.0.63802-0 , PubMed 16403879 )
#31556	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 #27846
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Dokdonella koreensis (DSM 17203, KCTC 12396, DS-123)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001632775

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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