Dyella japonica (DSM 101096, A8)

Name: Dyella japonica (DSM 101096, A8)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131709

Type strain

Strain Designation A8

Culture col. no. DSM 101096 A8

NCBI tax ID(s) 231455

Special Collections DSMZ

History <- J.-W. Chen, Microbiome Laboratory, University of Malaya; A8

Links

Dyella japonica A8 is a bacterium that was isolated from soil.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 407094

DSM 101096

@ref 20215

Last LPSN update 2026-02-09 11:31:32

Domain Bacteria

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
17453	D. japonica XD53, DSM 16301, ATCC BAA-939, IAM 15069, ... (type strain)
163220	D. japonica JCM 21528, IAM 15067, NBRC 104185
163221	D. japonica JCM 21529, IAM 15068, NBRC 104186

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	98
125439	negative	92

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
23505	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)
23505	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	92.1

Spore formation

@ref	Spore formation	Confidence
125439		97.1

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	Latitude	Longitude
23505	soil	Rimba Ilmu	Malaysia	MYS	Asia	3.1333	101.65 3.1333/101.65

Taxonmaps

69479

Global distribution of 16S sequence JX081589 (>99% sequence identity) for Dyella from Microbeatlas

Aquatic Samples	133
Soil Samples	980
Animal Samples	188
Plant Samples	138
Total Samples	1439

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
23505	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	ASM72538v1 assembly for Dyella japonica A8	complete	GCA_000725385	1217721.7	2588253754	1217721	98.94
66792	ASM29226v1 assembly for Dyella japonica A8	contig	GCA_000292265	1217721.3	2551306479	1217721	42.2

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
23505	Dyella japonica strain A8 16S ribosomal RNA gene, partial sequence	JX081589	1500		1217721

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Dyella japonica A8
PATRIC: 1217721.7

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	92.10	no
125439	gram_stain	BacteriaNetⓘ	negative	92.00	no
125439	motility	BacteriaNetⓘ	yes	78.30	no
125439	spore_formation	BacteriaNetⓘ	no	97.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Dyella japonica A8 A8
NCBI: GCA_000725385.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.00	no
125438	anaerobic	anaerobicⓘ	no	97.57	no
125438	aerobic	aerobicⓘ	yes	87.99	no
125438	spore-forming	spore-formingⓘ	no	89.75	no
125438	thermophilic	thermophileⓘ	no	97.00	yes
125438	flagellated	motile2+ⓘ	yes	73.27	no

Literature

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 )
#23505	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 101096
#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) .
#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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