Name: Diaphorobacter oryzae RF3
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 2957

Type strain:

Species: Diaphorobacter oryzae

Strain Designation: RF3

Culture col. no.: DSM 22780, KCTC 22225, LMG 24467

Strain history: <- SK Rhee, Chungbuk Natl. Univ.

NCBI tax ID(s): 1121478 (strain), 491745 (species)

SI-ID 323909

LMG 24467, KCTC 22225, DSM 22780

Special Collections

Section

When using BacDive for research please cite our paper

Diaphorobacter oryzae RF3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from thiosulfate-oxidizing enrichment culture from paddy soils.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Comamonadaceae*
	Genus	*Diaphorobacter*
	Species	**Diaphorobacter oryzae**
	Full Scientific Name (LPSN)	Diaphorobacter oryzae Pham et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #28923]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %94.6

[Ref.: #28923]	Cell length	1.55 µm

[Ref.: #28923]	Cell width	0.65 µm

[Ref.: #28923]	Cell shape	rod-shaped

[Ref.: #28923]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16513]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #16513]

Culture medium growth

[Ref.: #16513]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16513]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16513]	growth	28 °C
[Ref.: #28923]	growth	07-35 °C
[Ref.: #28923]	optimum	30 °C
[Ref.: #67771]	growth	25 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #28923]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #125439]

Ability of spore formation

no Confidence in %96.5

[Ref.: #28923]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #28923]	2-dehydro-D-gluconate ChEBI	+	carbon source
[Ref.: #28923]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #28923]	4-hydroxybenzoate ChEBI	+	carbon source
[Ref.: #28923]	acetate ChEBI	+	carbon source
[Ref.: #28923]	alanine ChEBI	+	carbon source
[Ref.: #28923]	decanoate ChEBI	+	carbon source
[Ref.: #28923]	gluconate ChEBI	+	carbon source
[Ref.: #28923]	glucose ChEBI	+	carbon source
[Ref.: #28923]	histidine ChEBI	+	carbon source
[Ref.: #28923]	lactate ChEBI	+	carbon source
[Ref.: #28923]	malate ChEBI	+	carbon source
[Ref.: #28923]	nitrate ChEBI	+	reduction
[Ref.: #28923]	proline ChEBI	+	carbon source
[Ref.: #28923]	propionate ChEBI	+	carbon source
[Ref.: #28923]	serine ChEBI	+	carbon source
[Ref.: #28923]	valerate ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #28923]	catalase	+	1.11.1.6
[Ref.: #28923]	cytochrome oxidase	+	1.9.3.1
[Ref.: #28923]	urease	+	3.5.1.5

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

[Ref.: #16513]	Sample type/isolated from	thiosulfate-oxidizing enrichment culture from paddy soils
[Ref.: #16513]	Geographic location (country and/or sea, region)	Cheongju
[Ref.: #16513]	Country	Republic of Korea
[Ref.: #16513]	Country ISO 3 Code	KOR
[Ref.: #16513]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From a thiosulfate-oxidizing enrichment culture
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Field
#Engineered	#Laboratory	#Lab enrichment
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EU342381 (>99% sequence identity) for Diaphorobacter oryzae from Microbeatlas

Aquatic Samples	183
Soil Samples	16
Animal Samples	13
Plant Samples	11
Total Samples	223

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

[Ref.: #16513]

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.: #16513]	Diaphorobacter oryzae strain RF3 16S ribosomal RNA gene, partial sequence	EU342381	1401	GenBank ENA	491745 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Diaphorobacter oryzae DSM 22780	2574179700	draft	JGI IMG/M	1121478 tax ID	*

[Ref.: #16513]	GC-content	62.9 mol%	high performance liquid chromatography (HPLC)
[Ref.: #28923]	GC-content	62.9 mol%

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

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Diaphorobacter oryzae DSM 22780 IMG: 2574179700
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	96.5
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	88.4
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	94.6
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	72.7

Availability in culture collections External links

[Ref.: #16513]

Culture collection no.

DSM 22780, KCTC 22225, LMG 24467

[Ref.: #72479]

SI-ID 323909

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Diaphorobacter oryzae sp. nov., isolated from a thiosulfate-oxidizing enrichment culture.	Pham VH, Park SJ, Roh Y, Roh DH, Rhee SK	Int J Syst Evol Microbiol	10.1099/ijs.0.001669-0	2009	*

References

#16513

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22780

#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 )

#28923

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 #25362 (see below)

#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) .

#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 .

#72479

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-ID323909.1 )

#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 .

#25362

IJSEM 218 2009 ( DOI 10.1099/ijs.0.001669-0 , PubMed 19196757 )

* These data were automatically processed and therefore are not curated

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Diaphorobacter oryzae DSM 22780

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