Dyella kyungheensis (DSM 100356, JCM 18747, KACC 16981)

Name: Dyella kyungheensis (DSM 100356, JCM 18747, KACC 16981)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130847

Type strain

Strain Designation THG-B117

Culture col. no. DSM 100356 JCM 18747 KACC 16981 THG-B117

NCBI tax ID(s) 1242174

Special Collections DSMZ JCM Literature strains

Links

Dyella kyungheensis THG-B117 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from soil of a cornus fruit field.

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

Name and taxonomic classification

SI-ID 406882

JCM 18747,DSM 100356

@ref 20215

Last LPSN update 2025-12-16 10:01:06

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Rhodanobacteraceae

Genus Dyella

Species Dyella kyungheensis

Full scientific name Dyella kyungheensis Son et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
31065	negative	2.75 µm	0.6 µm	rod-shaped
125438	negative					98.5

Pigmentation

31065

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21581	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
21581	positive	growth	28	mesophilic
31065	positive	optimum	27.5	mesophilic
67770	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH
31065	positive	optimum	7

Physiology and metabolism

Oxygen tolerance

31065

Oxygen toleranceaerobe

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31065	NaCl	positive	growth	0-2 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
31065	5291 ChEBI	gelatin	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
31065	17234 ChEBI	glucose	+	carbon source
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
31065	17814 ChEBI	salicin	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
31065	alkaline phosphatase	+	3.1.3.1
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
31065	catalase	+	1.11.1.6
31065	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
21581	+	-	-	-	-	+	-	+	+	-	+	-	+	+	-	-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Shrub (Scrub)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
21581	soil of a cornus fruit field	Hoengseong province	Republic of Korea	KOR	Asia
67770	Soil of a cornus fruit field of Hoengseong Province		Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence JX566987 (>99% sequence identity) for Dyella from Microbeatlas

Aquatic Samples	143
Soil Samples	2327
Animal Samples	282
Plant Samples	209
Total Samples	2961

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21581	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1690500v1 assembly for Dyella kyungheensis THG-B117	contig	GCA_016905005	1242174.3	3002279264	1242174	72.44

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21581	Dyella kyungheensis strain THG-B117 16S ribosomal RNA gene, partial sequence	JX566987	1454		1242174

GC content

21581

GC-content (mol%)64.8

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Dyella kyungheensis THG-B117
NCBI: GCA_016905005.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	yes
125438	anaerobic	anaerobicⓘ	no	97.61	yes
125438	aerobic	aerobicⓘ	yes	87.59	yes
125438	spore-forming	spore-formingⓘ	no	86.98	no
125438	thermophilic	thermophileⓘ	no	97.00	yes
125438	flagellated	motile2+ⓘ	yes	72.54	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Dyella agri sp. nov., isolated from reclaimed grassland soil.	Chaudhary DK, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002291	2017
Phylogeny	Dyella kyungheensis sp. nov., isolated from soil of a cornus fruit field.	Son HM, Yang JE, Yi EJ, Park Y, Won KH, Kim JH, Han CK, Kook M, Yi TH	Int J Syst Evol Microbiol	10.1099/ijs.0.051185-0	2013

References

#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 )
#21581	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100356
#27394	IJSEM 3807 2013 ( DOI 10.1099/ijs.0.051185-0 , PubMed 23667147 )
#31065	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 #27394
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68369	Automatically annotated from API 20NE .
#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 )
#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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Dyella kyungheensis (DSM 100356, JCM 18747, KACC 16981)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_016905005

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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