Dyadobacter soli (DSM 25329, JCM 16232, KCTC 22481)

Name: Dyadobacter soli (DSM 25329, JCM 16232, KCTC 22481)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23880

Type strain

Strain Designation MJ20

Culture col. no. DSM 25329 JCM 16232 KCTC 22481 MJ20

NCBI tax ID(s) 659014

Special Collections DSMZ JCM KCTC Literature strains

History <- JCM <- M.-J. Lee, KRIBB M. J. Lee MJ20. <- MJ Lee, H-Plus Eco, Korea [6658]

Links

Dyadobacter soli MJ20 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from farm soil.

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

Name and taxonomic classification

SI-ID 404040

KCTC 22481,JCM 16232,DSM 25329

@ref 20215

Last LPSN update 2026-02-09 11:23:50

Domain Bacteria

Phylum Bacteroidota

Class Cytophagia

Order Cytophagales

Family Spirosomataceae

Genus Dyadobacter

Species Dyadobacter soli

Full scientific name Dyadobacter soli Lee et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29732	negative	1.9-2.4 µm	0.6-0.7 µm	rod-shaped
67771				rod-shaped
67771	negative
125438					90.125
125438	negative				97.851
125439	negative				99.8

Pigmentation

29732

Productionyes

Multimedia

@ref:	20532
multimedia content:	DSM_25329.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_25329.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20532	REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)		Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) 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)
20532	positive	growth	28
29732	positive	growth	15-30
29732	positive	optimum	25
67770	positive	growth	25
67771	positive	growth	25

Culture pH

@ref	Ability	Type	PH
29732	positive	optimum	6.5-7
29732	positive	growth	05-08

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29732	aerobe
67771	aerobe
125439	obligate aerobe	94

Spore formation

@ref	Spore formation	Confidence
125439		99.2

Observation

@ref	Observation
29732	aggregates in chains
67770	quinones: MK-7
67771	quinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29732	16808 ChEBI	2-dehydro-D-gluconate	+	carbon source
29732	22599 ChEBI	arabinose	+	carbon source
29732	17234 ChEBI	glucose	+	carbon source
29732	25115 ChEBI	malate	+	carbon source
29732	17306 ChEBI	maltose	+	carbon source
29732	37684 ChEBI	mannose	+	carbon source
29732	28053 ChEBI	melibiose	+	carbon source
29732	506227 ChEBI	N-acetylglucosamine	+	carbon source
29732	18401 ChEBI	phenylacetate	+	carbon source
29732	26546 ChEBI	rhamnose	+	carbon source
29732	17992 ChEBI	sucrose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29732	catalase	+	1.11.1.6
29732	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Engineered	#Agriculture	#Field
#Engineered	#Food production	#Aquaculture

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
20532	farm soil	near Daejeon	Republic of Korea	KOR	Asia
67770	Farm soil near Daejeon		Republic of Korea	KOR	Asia
67771	From soil		Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence GQ241324 (>99% sequence identity) for Dyadobacter from Microbeatlas

Aquatic Samples	233
Soil Samples	517
Animal Samples	2781
Plant Samples	312
Total Samples	3843

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20532	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	IMG-taxon 2619619010 annotated assembly for Dyadobacter soli DSM 25329	scaffold	GCA_900101885	659014.3	2619619010	659014	67.84

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20532	Dyadobacter soli strain MJ20 16S ribosomal RNA gene, partial sequence	GQ241324	1398		659014

GC content

@ref	GC-content (mol%)	Method
20532	48.5	high performance liquid chromatography (HPLC)
29732	48.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Dyadobacter soli DSM 25329
NCBI: GCA_900101885

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.20	no
125439	motility	BacteriaNetⓘ	no	70.10	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Dyadobacter soli strain DSM 25329
PATRIC: 659014.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.85	yes
125438	anaerobic	anaerobicⓘ	no	99.22	yes
125438	spore-forming	spore-formingⓘ	no	81.38	no
125438	aerobic	aerobicⓘ	yes	89.53	yes
125438	thermophilic	thermophileⓘ	no	97.84	yes
125438	flagellated	motile2+ⓘ	no	90.13	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Dyadobacter endophyticus sp. nov., an endophytic bacterium isolated from maize root.	Gao JL, Sun P, Wang XM, Qiu TL, Lv FY, Yuan M, Yang MM, Sun JG	Int J Syst Evol Microbiol	10.1099/ijsem.0.001304	2016
Phylogeny	Dyadobacter jiangsuensis sp. nov., a methyl red degrading bacterium isolated from a dye-manufacturing factory.	Wang L, Chen L, Ling Q, Li CC, Tao Y, Wang M	Int J Syst Evol Microbiol	10.1099/ijs.0.000069	2015
Phylogeny	Dyadobacter soli sp. nov., a starch-degrading bacterium isolated from farm soil.	Lee M, Woo SG, Park J, Yoo SA	Int J Syst Evol Microbiol	10.1099/ijs.0.019653-0	2009
Phylogeny	Dyadobacter luticola sp. nov., isolated from a sewage sediment sample.	Song Z, Song Y, Yu Y, Choi L, Wang G, Li M	Int J Syst Evol Microbiol	10.1099/ijsem.0.003178	2018

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 )
#20532	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25329
#26114	IJSEM 2577 2010 ( DOI 10.1099/ijs.0.019653-0 , PubMed 20008109 )
#29732	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 #26114
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Dyadobacter soli (DSM 25329, JCM 16232, KCTC 22481)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Multimedia

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_900101885

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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