Dyella japonica (DSM 16301, ATCC BAA-939, IAM 15069)

Name: Dyella japonica (DSM 16301, ATCC BAA-939, IAM 15069)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17453

Type strain

Strain Designation XD53

Culture col. no. DSM 16301 ATCC BAA-939 IAM 15069 CCUG 58062 JCM 21530 2 more

NCBI tax ID(s) 1440762 231455

Special Collections DSMZ CCUG JCM Literature strains

Links

Dyella japonica XD53 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from soil.

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

Name and taxonomic classification

SI-ID 138000

ATCC BAA-939,DSM 16301,IAM 15069,BCRC 17596,CCRC 17596,JCM 21530,NBRC 102414,CCUG 58062

@ref 20215

Last LPSN update 2025-12-16 09:51:06

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Rhodanobacteraceae

Genus Dyella

Species Dyella japonica

Full scientific name Dyella japonica Xie and Yokota 2005

BacDive ID	Other strains from **Dyella japonica** (3)	Type strain
131709	D. japonica A8, DSM 101096
163220	D. japonica JCM 21528, IAM 15067, NBRC 104185
163221	D. japonica JCM 21529, IAM 15068, NBRC 104186

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31351	negative	1.2 µm	0.4 µm	rod-shaped
125438	negative				98.228
125439	negative				99.1

Pigmentation

31351

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6351	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
6351	CASO AGAR (MERCK 105458) (DSMZ Medium 220)	Medium recipe at MediaDive	Name: CASO AGAR (MERCK 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
6351	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6351	positive	growth	30	mesophilic
6351	positive	growth	28
31351	positive	growth	10-37
31351	positive	optimum	27.5	mesophilic
61583	positive	growth	30	mesophilic
67770	positive	growth	25	mesophilic

Culture pH

@ref	Ability	Type	PH
31351	positive	optimum	6.85
31351	positive	growth	5.6-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31351	aerobe
61583	aerobe
125439	aerobe	96.3

Spore formation

@ref	Spore formation	Confidence
125439		98.8

Observation

@ref	Observation
31351	aggregates in clumps
67770	quinones: Q-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31351	28757 ChEBI	fructose	+	carbon source
31351	17234 ChEBI	glucose	+	carbon source
31351	25017 ChEBI	leucine	+	carbon source
31351	17306 ChEBI	maltose	+	carbon source
31351	37684 ChEBI	mannose	+	carbon source
31351	506227 ChEBI	N-acetylglucosamine	+	carbon source
31351	17632 ChEBI	nitrate	+	reduction

Enzymes

@ref	Value	Activity	Ec
31351	acid phosphatase	+	3.1.3.2
31351	alkaline phosphatase	+	3.1.3.1
31351	catalase	+	1.11.1.6

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
6351	soil	Tokyo	Japan	JPN	Asia
61583	Soil	Tokyo	Japan	JPN	Asia
67770	Soil	Tokyo	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB110498 (>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
6351	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
67770	ASM101035v1 assembly for Dyella japonica DSM 16301	contig	GCA_001010355	1440762.4	2639762820	1440762	21

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6351	Dyella japonica gene for 16S ribosomal RNA, partial sequence, strain:XD53	AB110498	1485		231455
124043	Dyella japonica gene for 16S rRNA, partial sequence, strain: NBRC 102414.	AB681770	1465		231455

GC content

@ref	GC-content (mol%)	Method
6351	63.5
31351	63.7
67770	63.5	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Dyella japonica DSM 16301
NCBI: GCA_001010355

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.80	no
125439	motility	BacteriaNetⓘ	yes	85.70	no
125439	gram_stain	BacteriaNetⓘ	negative	99.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	96.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Dyella japonica DSM 16301
PATRIC: 1440762.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.23	yes
125438	anaerobic	anaerobicⓘ	no	92.56	yes
125438	spore-forming	spore-formingⓘ	no	86.04	no
125438	aerobic	aerobicⓘ	yes	84.60	yes
125438	thermophilic	thermophileⓘ	no	95.33	yes
125438	flagellated	motile2+ⓘ	yes	63.75	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Phylogenomics insights into order and families of Lysobacterales.	Kumar S, Bansal K, Patil PP, Patil PB.	Access Microbiol	10.1099/acmi.0.000015	2019
Genetics	Dyella humicola sp. nov., Dyella subtropica sp. nov., Dyella silvatica sp. nov. and Dyella silvae sp. nov., isolated from subtropical forest soil.	Feng GD, Deng X, Li J, Chen W, Zhang X, Zhu H.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005878	2023
Phylogeny	Dyella amyloliquefaciens sp. nov., isolated from forest soil.	Fu JC, Gao ZH, Wu TT, Chen MH, Qiu LH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003660	2019
Phylogeny	Dyella solisilvae sp. nov., isolated from mixed pine and broad-leaved forest soil.	Gao ZH, Yang Z, Chen MH, Huang ZJ, Qiu LH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003218	2019
Phylogeny	Rhodanobacter panaciterrae sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a ginseng field.	Wang L, An DS, Kim SG, Jin FX, Lee ST, Im WT	Int J Syst Evol Microbiol	10.1099/ijs.0.025718-0	2011
Phylogeny	Dyella ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea.	Jung HM, Ten LN, Kim KH, An DS, Im WT, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.64514-0	2009
Phylogeny	Rhodanobacter spathiphylli sp. nov., a gammaproteobacterium isolated from the roots of Spathiphyllum plants grown in a compost-amended potting mix.	De Clercq D, Van Trappen S, Cleenwerck I, Ceustermans A, Swings J, Coosemans J, Ryckeboer J	Int J Syst Evol Microbiol	10.1099/ijs.0.64131-0	2006
Phylogeny	Dyella japonica gen. nov., sp. nov., a gamma-proteobacterium isolated from soil.	Xie CH, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.63377-0	2005

References

#6351	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16301
#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 )
#31351	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 #27664 (see below)
#61583	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 58062
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Dyella japonica (DSM 16301, ATCC BAA-939, IAM 15069)

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_001010355

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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