Name: Dyella japonica XD53
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17453

Type strain:

Species: Dyella japonica

Strain Designation: XD53

Culture col. no.: DSM 16301, ATCC BAA-939, IAM 15069, CCUG 58062, JCM 21530, NBRC 102414

Strain history: IAM 15069 <-- C.-H. Xie XD53.

NCBI tax ID(s): 1440762 (strain), 231455 (species)

SI-ID 138000

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

Special Collections

Other strains from Dyella japonica

Section

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

Gram-negative
motile
rod-shaped
aerobe
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	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Rhodanobacteraceae*
	Genus	*Dyella*
	Species	**Dyella japonica**
	Full Scientific Name (LPSN)	Dyella japonica Xie and Yokota 2005

Information on morphological and physiological properties Morphology

[Ref.: #31351]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %98.228

[Ref.: #31351]	Cell length	1.2 µm

[Ref.: #31351]	Cell width	0.4 µm

[Ref.: #31351]	Cell shape	rod-shaped

[Ref.: #31351]	Motility	yes

[Ref.: #31351]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6351]

Culture medium

REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)

[Ref.: #6351]

Culture medium growth

[Ref.: #6351]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6351]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #6351]	growth	30 °C
[Ref.: #31351]	growth	10-37 °C
[Ref.: #31351]	optimum	27.5 °C
[Ref.: #61583]	growth	30 °C
[Ref.: #67770]	growth	25 °C

	pH	Kind of pH		pH
[Ref.: #31351]			optimum	6.85
[Ref.: #31351]			growth	5.6-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31351]	Oxygen tolerance	aerobe
[Ref.: #61583]	Oxygen tolerance	aerobe

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

[Ref.: #31351]	Observation	aggregates in clumps
[Ref.: #67770]	Observation	quinones: Q-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31351]	fructose ChEBI	+	carbon source
[Ref.: #31351]	glucose ChEBI	+	carbon source
[Ref.: #31351]	leucine ChEBI	+	carbon source
[Ref.: #31351]	maltose ChEBI	+	carbon source
[Ref.: #31351]	mannose ChEBI	+	carbon source
[Ref.: #31351]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #31351]	nitrate ChEBI	+	reduction

	Enzyme	Enzyme activity	EC number
[Ref.: #31351]	acid phosphatase	+	3.1.3.2
[Ref.: #31351]	alkaline phosphatase	+	3.1.3.1
[Ref.: #31351]	catalase	+	1.11.1.6

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

[Ref.: #6351]	Sample type/isolated from	soil
[Ref.: #6351]	Geographic location (country and/or sea, region)	Tokyo
[Ref.: #6351]	Country	Japan
[Ref.: #6351]	Country ISO 3 Code	JPN
[Ref.: #6351]	Continent	Asia

[Ref.: #61583]	Sample type/isolated from	Soil
[Ref.: #61583]	Geographic location (country and/or sea, region)	Tokyo
[Ref.: #61583]	Country	Japan
[Ref.: #61583]	Country ISO 3 Code	JPN
[Ref.: #61583]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil
[Ref.: #67770]	Geographic location (country and/or sea, region)	Tokyo
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #6351]

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.: #6351]	Dyella japonica gene for 16S ribosomal RNA, partial sequence, strain:XD53	AB110498	1485	GenBank ENA	231455 tax ID
[Ref.: #124043]	Dyella japonica gene for 16S rRNA, partial sequence, strain: NBRC 102414.	AB681770	1465	GenBank ENA	231455 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Dyella japonica DSM 16301	GCA_001010355	contig	GenBank ENA	1440762 tax ID
[Ref.: #66792]	Dyella japonica DSM 16301	1440762.4	wgs	PATRIC	1440762 tax ID	*
[Ref.: #66792]	Dyella japonica DSM 16301	2639762820	draft	JGI IMG/M	1440762 tax ID	*

[Ref.: #6351]	GC-content	63.5 mol%
[Ref.: #31351]	GC-content	63.7 mol%
[Ref.: #67770]	GC-content	63.5 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Dyella japonica DSM 16301 PATRIC: 1440762.4
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Dyella japonica DSM 16301 PATRIC: 1440762.4
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98.228	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	92.563	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	86.037	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	84.596	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95.333	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	63.747	no

Availability in culture collections External links

[Ref.: #6351]

Culture collection no.

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

[Ref.: #86449]

SI-ID 138000

Literature:

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

Topic	Title	Authors	Journal	DOI	Year
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

#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;

#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 )

#86449

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-ID138000.1 )

#124043

Dr. Isabel Schober, Dr. Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

#27664

IJSEM 753 2005 ( DOI 10.1099/ijs.0.63377-0 , PubMed 15774657 )

* These data were automatically processed and therefore are not curated

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Dyella japonica DSM 16301

Dyella japonica DSM 16301

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